{"title": "Sample and File Nomenclature", "status": "open", "content": [{"file": "/docs/public/smaht_nomenclature.rst", "status": "open", "options": {"filetype": "rst", "collapsible": false, "default_open": true, "convert_ext_links": true}, "consortia": [{"display_title": "SMaHT", "@type": ["Consortium", "Item"], "status": "open", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "identifier": "smaht_nomenclature", "date_created": "2024-03-01T19:21:13.991917+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2026-03-28T15:48:30.370034+00:00"}, "schema_version": "1", "submission_centers": [{"display_title": "HMS DAC", "uuid": "9626d82e-8110-4213-ac75-0a50adf890ff", "status": "open", "@id": "/submission-centers/9626d82e-8110-4213-ac75-0a50adf890ff/", "@type": ["SubmissionCenter", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/static-sections/e88a8a3d-cee8-430e-bfed-5c056bc384ea/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "e88a8a3d-cee8-430e-bfed-5c056bc384ea", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "smaht_nomenclature", "content_as_html": "<div class=\"rst-container\"><h2>SMaHT Sample and File Nomenclature</h2><h3>Overview</h3><p>The SMaHT sample and file names are the primary identifiers of biosamples from the Tissue Procurement Center (TPC) and files generated by the Data Analysis Center (DAC) of the SMaHT Network (\u201cNetwork\u201d).</p><p>The SMaHT sample and file names contain identifiers that are unique and immovable, as well as semi-human-readable codes that correspond to metadata. This document describes the naming schema and tables of codes for each metadata type that are included in sample and file names. The metadata fields in the sample and file names are delimited by a hyphen (\u201c-\u201d). \u201c#\u201d indicates a single-digit integer number, and \u201cA\u201d indicates an alphabetical letter in this document.</p><h3>Schema Documentation</h3><div class=\"table-responsive\"><table class=\"table table-borderless table-sm text-center\"><thead class=\"thead-smaht\"><tr><th>Download</th><th>Version</th><th>Release date</th><th>Filename</th></tr></thead><tbody class=\"table-border-inner\"><tr><td><a download=\"\" href=\"/static/files/SMaHT Sample and File Nomenclature v2.1.pdf\"><i class=\"icon fas icon-file-pdf text-danger icon-lg\"></i></a></td><td>2.1 (latest)</td><td>01/02/2026</td><td><a download=\"\" href=\"/static/files/SMaHT Sample and File Nomenclature v2.1.pdf\">SMaHT Sample and File Nomenclature v2.1.pdf</a></td></tr></tbody></table></div><h3>Part 1: Sample Schema and Protocol ID Tables</h3><h4>Naming Schema</h4><img alt=\"Nomenclature Part 1\" class=\"grey-border\" src=\"/static/img/Nomenclature_Part1.png\"/><h4>Table 1. Benchmarking cell line codes.</h4><div class=\"table-responsive\"><table class=\"table table-sm text-start\"><thead class=\"thead-smaht table-borderless\"><tr><th>Kit/Sample ID</th><th>Cell line description</th></tr></thead><tbody class=\"table-border-inner\"><tr><td>COLO829T</td><td>COLO829 tumor cell line</td></tr><tr><td>COLO829BL</td><td>COLO829BL normal lymphoblast cell line</td></tr><tr><td>COLO829BLT50</td><td>COLO829 1:50 admixture</td></tr><tr><td>HAPMAP6</td><td>Cell admixture of six HapMap cell lines</td></tr><tr><td>LBLA2</td><td>LB-LA2 fibroblast cell line</td></tr><tr><td>LBIPSC1</td><td>iPSC line from clone #1 derived from the LB-LA2 fibroblast cell line</td></tr><tr><td>LBIPSC2</td><td>iPSC line from clone #2 derived from the LB-LA2 fibroblast cell line</td></tr><tr><td>LBIPSC4</td><td>iPSC line from clone #4 derived from the LB-LA2 fibroblast cell line</td></tr><tr><td>LBIPSC52</td><td>iPSC line from clone #52 derived from the LB-LA2 fibroblast cell line</td></tr><tr><td>LBIPSC60</td><td>iPSC line from clone #60 derived from the LB-LA2 fibroblast cell line</td></tr></tbody></table></div><h4>Table 2A. Protocol IDs for SMaHT benchmarking tissues.</h4><div class=\"table-responsive\"><table class=\"table table-striped table-sm text-start\"><thead class=\"thead-smaht table-borderless\"><tr><th style=\"min-width:95px\">Protocol ID</th><th style=\"min-width:200px\">Tissue Name for Container</th><th style=\"min-width:200px\">Preservation</th><th style=\"min-width:200px\">Notes</th></tr></thead><tbody class=\"table-border-inner\"><tr><td>1A</td><td>Liver</td><td>Snap Frozen</td><td>Homogenate and non-homogenate samples</td></tr><tr><td class=\"text-secondary fst-italic\">1B</td><td class=\"text-secondary fst-italic\">unassigned</td><td class=\"text-secondary fst-italic\">N/A</td><td></td></tr><tr><td>1C</td><td>Liver</td><td>Fixed</td><td></td></tr><tr><td>1D</td><td>Lung</td><td>Snap Frozen</td><td>Homogenate and non-homogenate samples</td></tr><tr><td class=\"text-secondary fst-italic\">1E</td><td class=\"text-secondary fst-italic\">unassigned</td><td class=\"text-secondary fst-italic\">N/A</td><td></td></tr><tr><td>1F</td><td>Lung</td><td>Fixed</td><td></td></tr><tr><td>1G</td><td>Colon</td><td>Snap Frozen</td><td>Homogenate and non-homogenate samples</td></tr><tr><td class=\"text-secondary fst-italic\">1H</td><td class=\"text-secondary fst-italic\">unassigned</td><td class=\"text-secondary fst-italic\">N/A</td><td></td></tr><tr><td>1I</td><td>Colon</td><td>Fixed</td><td></td></tr><tr><td>1J</td><td>Skin</td><td>Snap Frozen</td><td>Tissue specimen (~10 cm)</td></tr><tr><td>1K</td><td>Skin</td><td>Snap Frozen</td><td>Tissue core from the intact tissue was made (~1 cm)</td></tr><tr><td>1L</td><td>Skin</td><td>Fixed</td><td></td></tr><tr><td class=\"text-secondary fst-italic\">1M/N/O/P</td><td class=\"text-secondary fst-italic\">unassigned</td><td class=\"text-secondary fst-italic\">N/A</td><td></td></tr><tr><td>1Q</td><td>Brain, Frontal Lobe</td><td>Snap Frozen</td><td>Homogenate and non-homogenate samples</td></tr></tbody></table></div><h4>Table 2B. Protocol IDs for SMaHT production tissues.</h4><div class=\"table-responsive\"><table class=\"table table-striped table-sm text-start\"><thead class=\"thead-smaht table-borderless\"><tr><th style=\"min-width:95px\">Protocol ID</th><th style=\"min-width:200px\">Tissue Name for Container</th><th style=\"min-width:200px\">Preservation</th></tr></thead><tbody class=\"table-border-inner\"><tr><td>3A</td><td>Blood, Whole</td><td>Snap Frozen</td></tr><tr><td>3B</td><td>Buccal Swab</td><td>Fresh</td></tr><tr><td>3C</td><td>Esophagus</td><td>Snap Frozen</td></tr><tr><td>3D</td><td>Esophagus</td><td>Fixed</td></tr><tr><td>3E</td><td>Colon, Ascending</td><td>Snap Frozen</td></tr><tr><td>3F</td><td>Colon, Ascending</td><td>Fixed</td></tr><tr><td>3G</td><td>Colon, Descending</td><td>Snap Frozen</td></tr><tr><td>3H</td><td>Colon, Descending</td><td>Fixed</td></tr><tr><td>3I</td><td>Liver Sample</td><td>Snap Frozen</td></tr><tr><td>3J</td><td>Liver Sample</td><td>Fixed</td></tr><tr><td>3K</td><td>Adrenal Gland, Left</td><td>Snap Frozen</td></tr><tr><td>3L</td><td>Adrenal Gland, Left</td><td>Fixed</td></tr><tr><td>3M</td><td>Adrenal Gland, Right</td><td>Snap Frozen</td></tr><tr><td>3N</td><td>Adrenal Gland, Right</td><td>Fixed</td></tr><tr><td>3O</td><td>Aorta, Abdominal</td><td>Snap Frozen</td></tr><tr><td>3P</td><td>Aorta, Abdominal</td><td>Fixed</td></tr><tr><td>3Q</td><td>Lung</td><td>Snap Frozen</td></tr><tr><td>3R</td><td>Lung</td><td>Fixed</td></tr><tr><td>3S</td><td>Heart, LV</td><td>Snap Frozen</td></tr><tr><td>3T</td><td>Heart, LV</td><td>Fixed</td></tr><tr><td>3U</td><td>Testis, Left</td><td>Snap Frozen</td></tr><tr><td>3V</td><td>Testis, Left</td><td>Fixed</td></tr><tr><td>3W</td><td>Testis, Right</td><td>Snap Frozen</td></tr><tr><td>3X</td><td>Testis, Right</td><td>Fixed</td></tr><tr><td>3Y</td><td>Ovary, Left</td><td>Snap Frozen</td></tr><tr><td>3Z</td><td>Ovary, Left</td><td>Fixed</td></tr><tr><td>3AA</td><td>Ovary, Right</td><td>Snap Frozen</td></tr><tr><td>3AB</td><td>Ovary, Right</td><td>Fixed</td></tr><tr><td>3AC*</td><td>Dermal Fibroblast</td><td>Cultured Cells</td></tr><tr><td>3AD</td><td>Skin, Calf</td><td>Snap Frozen</td></tr><tr><td>3AE</td><td>Skin, Calf</td><td>Fixed</td></tr><tr><td>3AF</td><td>Skin, Abdomen</td><td>Snap Frozen</td></tr><tr><td>3AG</td><td>Skin, Abdomen</td><td>Fixed</td></tr><tr><td>3AH</td><td>Muscle</td><td>Snap Frozen</td></tr><tr><td>3AI</td><td>Muscle</td><td>Fixed</td></tr><tr><td>3AJ</td><td>Brain</td><td>Fresh</td></tr><tr><td>3AK</td><td>Frontal Lobe, Brain, Left hemisphere</td><td>Snap Frozen</td></tr><tr><td>3AL</td><td>Temporal Lobe, Brain, Left hemisphere</td><td>Snap Frozen</td></tr><tr><td>3AM</td><td>Cerebellum, Brain, Left hemisphere</td><td>Snap Frozen</td></tr><tr><td>3AN</td><td>Hippocampus, Brain, Left hemisphere</td><td>Snap Frozen</td></tr><tr><td>3AO</td><td>Hippocampus, Brain, Right hemisphere</td><td>Snap Frozen</td></tr><tr><td>3AP</td><td>Frontal Lobe, Brain, Left hemisphere</td><td>Fixed</td></tr><tr><td>3AQ</td><td>Temporal Lobe, Brain, Left hemisphere</td><td>Fixed</td></tr><tr><td>3AR</td><td>Cerebellum, Brain, Left hemisphere</td><td>Fixed</td></tr><tr><td>3AS</td><td>Hippocampus, Brain, Left hemisphere</td><td>Fixed</td></tr><tr><td>3AT</td><td>Hippocampus, Brain, Right hemisphere</td><td>Fixed</td></tr></tbody></table></div><div class=\"line-block\"><div class=\"line\">* 3AC = Fibroblasts are isolated from fresh calf skin.</div></div><h3>Part 2: Base Schema, Platform, and Assay Codes</h3><img alt=\"Nomenclature Part 2\" class=\"grey-border\" src=\"/static/img/Nomenclature_Part2.png\"/><h4>Table 3A. Sequencing platform codes.</h4><div class=\"table-responsive\"><table class=\"table table-striped table-sm\"><thead class=\"thead-smaht table-borderless\"><tr><th class=\"text-center\" width=\"25%\">SMaHT code</th><th class=\"text-start\">Sequencing platform</th></tr></thead><tbody class=\"table-border-inner\"><tr><td class=\"text-center\">A</td><td class=\"text-start\">Illumina NovaSeq X, Illumina NovaSeq X Plus</td></tr><tr><td class=\"text-center\">B</td><td class=\"text-start\">PacBio Revio HiFi</td></tr><tr><td class=\"text-center\">C</td><td class=\"text-start\">Illumina NovaSeq 6000</td></tr><tr><td class=\"text-center\">D</td><td class=\"text-start\">ONT PromethION 24</td></tr><tr><td class=\"text-center\">E</td><td class=\"text-start\">ONT PromethION 2 Solo</td></tr><tr><td class=\"text-center\">F</td><td class=\"text-start\">ONT MinION Mk1B</td></tr><tr><td class=\"text-center\">G</td><td class=\"text-start\">Illumina HiSeq X</td></tr><tr><td class=\"text-center text-secondary fst-italic\">H [deprecated]</td><td class=\"text-start text-secondary fst-italic\">Illumina NovaSeq X Plus</td></tr><tr><td class=\"text-center\">I</td><td class=\"text-start\">BGI DNBSEQ-G400</td></tr><tr><td class=\"text-center\">J</td><td class=\"text-start\">Element AVITI</td></tr><tr><td class=\"text-center\">K</td><td class=\"text-start\">Illumina NextSeq 2000</td></tr><tr><td class=\"text-center\">L</td><td class=\"text-start\">PacBio Sequel IIe</td></tr><tr><td class=\"text-center\">M</td><td class=\"text-start\">Ultima Genomics UG 100</td></tr><tr><td class=\"cell-small-text text-start\">(set the codes as data are generated on different sequencing platforms and submitted to DAC)</td><td class=\"text-start\">PacBio Onso</td></tr></tbody></table></div><h4>Table 3B. Experimental assay codes.</h4><div class=\"table-responsive\"><table class=\"table table-sm text-start\"><thead class=\"thead-smaht table-borderless\"><tr><th>Code</th><th>Assay Name</th><th>Description</th></tr></thead><tbody class=\"table-border-inner\"><tr><td>000</td><td></td><td>(Null or not-applicable)</td></tr><tr class=\"table-stripe-secondary text-600 fst-italic\"><td colspan=\"3\">[001-100: DNA-based assays]</td></tr><tr><td>001</td><td>WGS</td><td>DNA, PCR-free, Bulk, Whole genome sequencing (WGS)</td></tr><tr><td>002</td><td>PCR WGS</td><td>DNA PCR, Bulk, WGS</td></tr><tr><td>003</td><td>Ultra-Long WGS</td><td>DNA, PCR-free, Bulk, Ultra-Long WGS</td></tr><tr><td>004</td><td>Fiber-seq</td><td>DNA, PCR-free, Bulk, Fiber-seq</td></tr><tr><td>005</td><td>Hi-C</td><td>DNA, Bulk, Hi-C</td></tr><tr><td>006</td><td>Bulk NTSeq</td><td>DNA, Bulk, NTSeq</td></tr><tr><td>007</td><td>CODEC</td><td>DNA, Bulk, Duplex-seq, CODEC</td></tr><tr><td>008</td><td>Bot-seq</td><td>DNA, Bulk, Duplex-seq, Bot-seq</td></tr><tr><td>009</td><td>NanoSeq</td><td>DNA, Bulk, Duplex-seq, NanoSeq</td></tr><tr><td>010</td><td>scNanoSeq</td><td>DNA, Single-cell, Duplex-seq, scNanoSeq</td></tr><tr><td>011</td><td>DLP+</td><td>DNA, Single-cell, DLP+</td></tr><tr><td>012</td><td>Microbulk MALBAC WGS</td><td>DNA, Microbulk, MALBAC-amplified WGS</td></tr><tr><td>013</td><td>Single-cell MALBAC WGS</td><td>DNA, Single-cell, MALBAC-amplified WGS</td></tr><tr><td>014</td><td>Microbulk PTA WGS</td><td>DNA, Microbulk, PTA-amplified WGS</td></tr><tr><td>015</td><td>Single-cell PTA WGS</td><td>DNA, Single-cell, PTA-amplified WGS</td></tr><tr><td>016</td><td>scDip-C</td><td>DNA, Single-cell, scDip-C</td></tr><tr><td>017</td><td>CompDuplex-seq</td><td>DNA, Bulk, Duplex-seq, CompDuplex-seq</td></tr><tr><td>018</td><td>scCompDuplex-seq</td><td>DNA, Single-cell, Duplex-seq, scCompDuplex-seq</td></tr><tr><td>019</td><td>Strand-seq</td><td>DNA, Bulk, Strand-seq</td></tr><tr><td>020</td><td>scStrand-seq</td><td>DNA, Single-cell, scStrand-seq</td></tr><tr><td>021</td><td>HiDEF-seq</td><td>DNA, Bulk, Duplex-seq, HiDEF-seq</td></tr><tr><td>022</td><td>HAT-seq</td><td>DNA, Bulk, HAT-seq</td></tr><tr><td>023</td><td>Microbulk HAT-seq</td><td>DNA, Microbulk, PTA-amplified HAT-seq</td></tr><tr><td>024</td><td>scHAT-seq</td><td>DNA, Single-cell, PTA-amplified, HAT-seq</td></tr><tr><td>025</td><td>VISTA-seq</td><td>DNA, Bulk, Duplex-seq, VISTA-seq</td></tr><tr><td>026</td><td>Microbulk VISTA-seq</td><td>DNA, Microbulk, Duplex-seq, VISTA-seq</td></tr><tr><td>027</td><td>scVISTA-seq</td><td>DNA, Single-cell, Duplex-seq, VISTA-seq</td></tr><tr><td>028</td><td>TEnCATS</td><td>DNA, Bulk, TEnCATS</td></tr><tr><td>029</td><td>L1-ONT</td><td>DNA, Bulk, L1-ONT</td></tr><tr><td>030</td><td>ppmSeq</td><td>DNA, Bulk, Duplex-seq, ppmSeq</td></tr><tr><td class=\"pb-3 pt-07\" colspan=\"3\"></td></tr><tr class=\"table-stripe-secondary fst-italic text-600\"><td colspan=\"3\">[101-200: RNA-based assays]</td></tr><tr><td>101</td><td>RNA-seq</td><td>RNA, Bulk, RNA-seq</td></tr><tr><td>102</td><td>Kinnex</td><td>RNA, Bulk, Kinnex</td></tr><tr><td>103</td><td>snRNA-seq</td><td>RNA, Single-cell, snRNA-seq</td></tr><tr><td>104</td><td>STORM-Seq</td><td>RNA, Single-cell, STORM-seq</td></tr><tr><td>105</td><td>Tranquil-Seq</td><td>RNA, Single-cell, Tranquil-seq</td></tr><tr><td class=\"pb-3 pt-07\" colspan=\"3\"></td></tr><tr class=\"table-stripe-secondary fst-italic text-600\"><td colspan=\"3\">[201-300: Chromatin-based assays]</td></tr><tr><td>201</td><td>ATAC-seq</td><td>Chromatin, Bulk, ATAC-seq</td></tr><tr><td>202</td><td>CUT&amp;Tag</td><td>Chromatin, Bulk, CUT&amp;Tag</td></tr><tr><td>203</td><td>varCUT&amp;Tag</td><td>Chromatin, Bulk, varCUT&amp;Tag</td></tr><tr><td>204</td><td>sc-varCUT&amp;Tag</td><td>Chromatin, Single-cell, sc-varCUT&amp;Tag</td></tr><tr><td class=\"pb-3 pt-07\" colspan=\"3\"></td></tr></tbody></table></div><h4>Table 4. SMaHT data generation center codes.</h4><div class=\"table-responsive\"><table class=\"table table-striped table-sm text-start\"><thead class=\"thead-smaht table-borderless\"><tr><th>Code</th><th>Category</th><th>Institute</th><th>Contact PI</th></tr></thead><tbody class=\"table-border-inner\"><tr><td>bcm</td><td>GCC</td><td>Baylor College of Medicine</td><td>Richard Gibbs</td></tr><tr><td>broad</td><td>GCC</td><td>Broad Institute</td><td>Kristin Ardlie</td></tr><tr><td>nygc</td><td>GCC</td><td>New York Genome Center</td><td>Soren Germer</td></tr><tr><td>uwsc</td><td>GCC</td><td>University of Washington &amp; Seattle Children\u2019s Hospital</td><td>Jimmy Bennett</td></tr><tr><td>washu</td><td>GCC</td><td>Washington University in St. Louis</td><td>Ting Wang</td></tr><tr><td>bcm1</td><td>TTD</td><td>Baylor College of Medicine</td><td>Chuck Zong</td></tr><tr><td>bcm2</td><td>TTD</td><td>Baylor College of Medicine</td><td>Fritz Sedlazeck</td></tr><tr><td>bch1</td><td>TTD</td><td>Boston Children\u2019s Hospital</td><td>Christopher Walsh</td></tr><tr><td>bch2</td><td>TTD</td><td>Boston Children\u2019s Hospital</td><td>Sangita Choudhury</td></tr><tr><td>broad1</td><td>TTD</td><td>Broad Institute</td><td>Fei Chen</td></tr><tr><td>cwru</td><td>TTD</td><td>Case Western Reserve University</td><td>Fulai Jin</td></tr><tr><td>dfci</td><td>TTD</td><td>Dana-Farber Cancer Institute</td><td>Kathleen Burns</td></tr><tr><td>mayo</td><td>TTD</td><td>Mayo Clinic</td><td>Alexej Arbyzov</td></tr><tr><td>nyu</td><td>TTD</td><td>New York University</td><td>Gilad Evrony</td></tr><tr><td>stfd</td><td>TTD</td><td>Stanford University</td><td>Alexander Urban</td></tr><tr><td>umass</td><td>TTD</td><td>University of Massachusetts</td><td>Thomas Fazzio</td></tr><tr><td>umich</td><td>TTD</td><td>University of Michigan</td><td>Ryan Mills</td></tr><tr><td>uutah</td><td>TTD</td><td>University of Utah</td><td>Gabor Marth</td></tr><tr><td>wcnygc</td><td>TTD</td><td>Weill Cornell Medicine &amp; New York Genome Center</td><td>Dan Landau</td></tr><tr><td>dac</td><td>DAC</td><td>Harvard Medical School</td><td>Peter Park</td></tr><tr><td>tpc</td><td>TPC</td><td>National Disease Research Interchange (NDRI)</td><td>Thomas Bell</td></tr></tbody></table></div><h3>Part 3: File Name breakdown</h3><img alt=\"Nomenclature Part 3\" class=\"grey-border\" src=\"/static/img/Nomenclature_Part3.png\"/><h4>Table 5. Genome version (A) and variant type (B) tables.</h4><div class=\"table-responsive\"><table class=\"table table-sm text-start\"><caption style=\"caption-side:top;\">(A)</caption><thead class=\"thead-smaht table-borderless\"><tr><th>Reference Genome</th><th>Code</th></tr></thead><tbody class=\"table-border-inner\"><tr><td>GRCh38 without ALT contigs</td><td>GRCh38</td></tr><tr><td>GRCh38 with ALT contigs</td><td>GRCh38_ALT</td></tr><tr><td>T2T CHM13</td><td>CHM13</td></tr><tr><td>Donor-specific genome assembly</td><td>DSA</td></tr></tbody></table><table class=\"table table-sm text-start\"><caption style=\"caption-side:top;\">(B)</caption><thead class=\"thead-smaht table-borderless\"><tr><th>Data Type</th><th>Code</th></tr></thead><tbody class=\"table-border-inner\"><tr><td>Reference conversion</td><td>[Source]To[Target]</td></tr><tr><td>Donor-specific genome assembly haplotype</td><td>hapX, hapY, hapX1, hapX2</td></tr><tr><td>Gene expression level</td><td>gene</td></tr><tr><td>Transcript isoform expression level or isoform information</td><td>isoform</td></tr><tr><td>Junction annotations</td><td>junction</td></tr><tr><td>Full-length, non-concatemer (FLNC) Kinnex reads</td><td>flnc</td></tr><tr><td>Aligned consensus Duplex-Seq BAM</td><td>consensus</td></tr></tbody></table></div><h3>Example Files with the SMaHT Nomenclature</h3><img alt=\"Nomenclature_ExampleFiles\" class=\"grey-border\" src=\"/static/img/Nomenclature_ExampleFiles.png\"/></div>", "content": "==================================\nSMaHT Sample and File Nomenclature\n==================================\n\n\nOverview\n--------\nThe SMaHT sample and file names are the primary identifiers of biosamples from the Tissue Procurement Center (TPC) and files generated by the Data Analysis Center (DAC) of the SMaHT Network (\u201cNetwork\u201d). \n\nThe SMaHT sample and file names contain identifiers that are unique and immovable, as well as semi-human-readable codes that correspond to metadata. This document describes the naming schema and tables of codes for each metadata type that are included in sample and file names. The metadata fields in the sample and file names are delimited by a hyphen (\u201c-\u201d). \u201c#\u201d indicates a single-digit integer number, and \u201cA\u201d indicates an alphabetical letter in this document.\n\n\nSchema Documentation\n--------------------\n\n.. raw:: html\n\n    <div class=\"table-responsive\"> \n        <table class=\"table table-borderless table-sm text-center\">\n            <thead class=\"thead-smaht\">\n                <tr>\n                    <th>Download</th>\n                    <th>Version</th>\n                    <th>Release date</th>\n                    <th>Filename</th>\n                </tr>\n            </thead>\n            <tbody class=\"table-border-inner\">\n                <tr>\n                    <td>\n                        <a href=\"/static/files/SMaHT Sample and File Nomenclature v2.1.pdf\" download>\n                            <i class=\"icon fas icon-file-pdf text-danger icon-lg\"></i>\n                        </a>\n                    </td>\n                    <td>2.1 (latest)</td>\n                    <td>01/02/2026</td>\n                    <td><a href=\"/static/files/SMaHT Sample and File Nomenclature v2.1.pdf\" download>SMaHT Sample and File Nomenclature v2.1.pdf</a></td>\n                </tr>\n            </tbody>\n        </table>\n    </div>\n\n\n\nPart 1: Sample Schema and Protocol ID Tables\n--------------------------------------------\n\n\n\nNaming Schema\n~~~~~~~~~~~~~\n\n.. raw:: html\n    \n    <img class=\"grey-border\" src=\"/static/img/Nomenclature_Part1.png\" alt=\"Nomenclature Part 1\"/>\n\n\nTable 1. Benchmarking cell line codes.\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n.. raw:: html\n\n    <div class=\"table-responsive\">\n        <table class=\"table table-sm text-start\">\n            <thead class=\"thead-smaht table-borderless\">\n                <tr>\n                    <th>Kit/Sample ID</th>\n                    <th>Cell line description</th>\n                </tr>\n            </thead>\n            <tbody class=\"table-border-inner\">\n                <tr>\n                    <td>COLO829T</td>\n                    <td>COLO829 tumor cell line</td>\n                </tr>\n                <tr>\n                    <td>COLO829BL</td>\n                    <td>COLO829BL normal lymphoblast cell line</td>\n                </tr>\n                <tr>\n                    <td>COLO829BLT50</td>\n                    <td>COLO829 1:50 admixture</td>\n                </tr>\n                <tr>\n                    <td>HAPMAP6</td>\n                    <td>Cell admixture of six HapMap cell lines</td>\n                </tr>\n                <tr>\n                    <td>LBLA2</td>\n                    <td>LB-LA2 fibroblast cell line</td>\n                </tr>\n                <tr>\n                    <td>LBIPSC1</td>\n                    <td>iPSC line from clone #1 derived from the LB-LA2 fibroblast cell line</td>\n                </tr>\n                <tr>\n                    <td>LBIPSC2</td>\n                    <td>iPSC line from clone #2 derived from the LB-LA2 fibroblast cell line</td>\n                </tr>\n                <tr>\n                    <td>LBIPSC4</td>\n                    <td>iPSC line from clone #4 derived from the LB-LA2 fibroblast cell line</td>\n                </tr>\n                <tr>\n                    <td>LBIPSC52</td>\n                    <td>iPSC line from clone #52 derived from the LB-LA2 fibroblast cell line</td>\n                </tr>\n                <tr>\n                    <td>LBIPSC60</td>\n                    <td>iPSC line from clone #60 derived from the LB-LA2 fibroblast cell line</td>\n                </tr>\n            </tbody>\n        </table>\n    </div>\n\n\nTable 2A. Protocol IDs for SMaHT benchmarking tissues.\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n.. raw:: html\n\n    <div class=\"table-responsive\">\n        <table class=\"table table-striped table-sm text-start\">\n            <thead class=\"thead-smaht table-borderless\">\n                <tr>\n                    <th style=\"min-width:95px\">Protocol ID</th>\n                    <th style=\"min-width:200px\">Tissue Name for Container</th>\n                    <th style=\"min-width:200px\">Preservation</th>\n                    <th style=\"min-width:200px\">Notes</th>\n                </tr>\n            </thead>\n            <tbody class=\"table-border-inner\">\n                <tr>\n                    <td>1A</td>\n                    <td>Liver</td>\n                    <td>Snap Frozen</td>\n                    <td>Homogenate and non-homogenate samples</td>\n                </tr>\n                <tr>\n                    <td class=\"text-secondary fst-italic\">1B</td>\n                    <td class=\"text-secondary fst-italic\">unassigned</td>\n                    <td class=\"text-secondary fst-italic\">N/A</td>\n                    <td></td>\n                </tr>\n                <tr>\n                    <td>1C</td>\n                    <td>Liver</td>\n                    <td>Fixed</td>\n                    <td></td>\n                </tr>\n                <tr>\n                    <td>1D</td>\n                    <td>Lung</td>\n                    <td>Snap Frozen</td>\n                    <td>Homogenate and non-homogenate samples</td>\n                </tr>\n                <tr>\n                    <td class=\"text-secondary fst-italic\">1E</td>\n                    <td class=\"text-secondary fst-italic\">unassigned</td>\n                    <td class=\"text-secondary fst-italic\">N/A</td>\n                    <td></td>\n                </tr>\n                <tr>\n                    <td>1F</td>\n                    <td>Lung</td>\n                    <td>Fixed</td>\n                    <td></td>\n                </tr>\n                <tr>\n                    <td>1G</td>\n                    <td>Colon</td>\n                    <td>Snap Frozen</td>\n                    <td>Homogenate and non-homogenate samples</td>\n                </tr>\n                <tr>\n                    <td class=\"text-secondary fst-italic\">1H</td>\n                    <td class=\"text-secondary fst-italic\">unassigned</td>\n                    <td class=\"text-secondary fst-italic\">N/A</td>\n                    <td></td>\n                </tr>\n                <tr>\n                    <td>1I</td>\n                    <td>Colon</td>\n                    <td>Fixed</td>\n                    <td></td>\n                </tr>\n                <tr>\n                    <td>1J</td>\n                    <td>Skin</td>\n                    <td>Snap Frozen</td>\n                    <td>Tissue specimen (~10 cm)</td>\n                </tr>\n                <tr>\n                    <td>1K</td>\n                    <td>Skin</td>\n                    <td>Snap Frozen</td>\n                    <td>Tissue core from the intact tissue was made (~1 cm)</td>\n                </tr>\n                <tr>\n                    <td>1L</td>\n                    <td>Skin</td>\n                    <td>Fixed</td>\n                    <td></td>\n                </tr>\n                <tr>\n                    <td class=\"text-secondary fst-italic\">1M/N/O/P</td>\n                    <td class=\"text-secondary fst-italic\">unassigned</td>\n                    <td class=\"text-secondary fst-italic\">N/A</td>\n                    <td></td>\n                </tr>\n                <tr>\n                    <td>1Q</td>\n                    <td>Brain, Frontal Lobe</td>\n                    <td>Snap Frozen</td>\n                    <td>Homogenate and non-homogenate samples</td>\n                </tr>\n            </tbody>\n        </table>\n    </div>\n\n\nTable 2B. Protocol IDs for SMaHT production tissues.\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n.. raw:: html\n\n    <div class=\"table-responsive\">\n        <table class=\"table table-striped table-sm text-start\">\n            <thead class=\"thead-smaht table-borderless\">\n                <tr>\n                    <th style=\"min-width:95px\">Protocol ID</th>\n                    <th style=\"min-width:200px\">Tissue Name for Container</th>\n                    <th style=\"min-width:200px\">Preservation</th>\n                </tr>\n            </thead>\n            <tbody class=\"table-border-inner\">\n                <tr>\n                    <td>3A</td>\n                    <td>Blood, Whole</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3B</td>\n                    <td>Buccal Swab</td>\n                    <td>Fresh</td>\n                </tr>\n                <tr>\n                    <td>3C</td>\n                    <td>Esophagus</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3D</td>\n                    <td>Esophagus</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3E</td>\n                    <td>Colon, Ascending</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3F</td>\n                    <td>Colon, Ascending</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3G</td>\n                    <td>Colon, Descending</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3H</td>\n                    <td>Colon, Descending</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3I</td>\n                    <td>Liver Sample</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3J</td>\n                    <td>Liver Sample</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3K</td>\n                    <td>Adrenal Gland, Left</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3L</td>\n                    <td>Adrenal Gland, Left</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3M</td>\n                    <td>Adrenal Gland, Right</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3N</td>\n                    <td>Adrenal Gland, Right</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3O</td>\n                    <td>Aorta, Abdominal</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3P</td>\n                    <td>Aorta, Abdominal</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3Q</td>\n                    <td>Lung</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3R</td>\n                    <td>Lung</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3S</td>\n                    <td>Heart, LV</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3T</td>\n                    <td>Heart, LV</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3U</td>\n                    <td>Testis, Left</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3V</td>\n                    <td>Testis, Left</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3W</td>\n                    <td>Testis, Right</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3X</td>\n                    <td>Testis, Right</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3Y</td>\n                    <td>Ovary, Left</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3Z</td>\n                    <td>Ovary, Left</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3AA</td>\n                    <td>Ovary, Right</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3AB</td>\n                    <td>Ovary, Right</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3AC*</td>\n                    <td>Dermal Fibroblast</td>\n                    <td>Cultured Cells</td>\n                </tr>\n                <tr>\n                    <td>3AD</td>\n                    <td>Skin, Calf</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3AE</td>\n                    <td>Skin, Calf</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3AF</td>\n                    <td>Skin, Abdomen</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3AG</td>\n                    <td>Skin, Abdomen</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3AH</td>\n                    <td>Muscle</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3AI</td>\n                    <td>Muscle</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3AJ</td>\n                    <td>Brain</td>\n                    <td>Fresh</td>\n                </tr>\n                <tr>\n                    <td>3AK</td>\n                    <td>Frontal Lobe, Brain, Left hemisphere</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3AL</td>\n                    <td>Temporal Lobe, Brain, Left hemisphere</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3AM</td>\n                    <td>Cerebellum, Brain, Left hemisphere</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3AN</td>\n                    <td>Hippocampus, Brain, Left hemisphere</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3AO</td>\n                    <td>Hippocampus, Brain, Right hemisphere</td>\n                    <td>Snap Frozen</td>\n                </tr>\n                <tr>\n                    <td>3AP</td>\n                    <td>Frontal Lobe, Brain, Left hemisphere</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3AQ</td>\n                    <td>Temporal Lobe, Brain, Left hemisphere</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3AR</td>\n                    <td>Cerebellum, Brain, Left hemisphere</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3AS</td>\n                    <td>Hippocampus, Brain, Left hemisphere</td>\n                    <td>Fixed</td>\n                </tr>\n                <tr>\n                    <td>3AT</td>\n                    <td>Hippocampus, Brain, Right hemisphere</td>\n                    <td>Fixed</td>\n                </tr>\n            </tbody>\n        </table>\n    </div>\n\n| \\* 3AC = Fibroblasts are isolated from fresh calf skin.\n\n\n\nPart 2: Base Schema, Platform, and Assay Codes\n----------------------------------------------\n\n.. raw:: html\n    \n    <img class=\"grey-border\" src=\"/static/img/Nomenclature_Part2.png\" alt=\"Nomenclature Part 2\"/>\n\n\n\nTable 3A. Sequencing platform codes.\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n.. raw:: html\n\n    <div class=\"table-responsive\">\n        <table class=\"table table-striped table-sm\">\n            <thead class=\"thead-smaht table-borderless\">\n                <tr>\n                    <th class=\"text-center\" width=\"25%\">SMaHT code</th>\n                    <th class=\"text-start\">Sequencing platform</th>\n                </tr>\n            </thead>\n            <tbody class=\"table-border-inner\">\n                <tr>\n                    <td class=\"text-center\">A</td>\n                    <td class=\"text-start\">Illumina NovaSeq X, Illumina NovaSeq X Plus</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">B</td>\n                    <td class=\"text-start\">PacBio Revio HiFi</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">C</td>\n                    <td class=\"text-start\">Illumina NovaSeq 6000</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">D</td>\n                    <td class=\"text-start\">ONT PromethION 24</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">E</td>\n                    <td class=\"text-start\">ONT PromethION 2 Solo</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">F</td>\n                    <td class=\"text-start\">ONT MinION Mk1B</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">G</td>\n                    <td class=\"text-start\">Illumina HiSeq X</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center text-secondary fst-italic\">H [deprecated]</td>\n                    <td class=\"text-start text-secondary fst-italic\">Illumina NovaSeq X Plus</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">I</td>\n                    <td class=\"text-start\">BGI DNBSEQ-G400</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">J</td>\n                    <td class=\"text-start\">Element AVITI</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">K</td>\n                    <td class=\"text-start\">Illumina NextSeq 2000</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">L</td>\n                    <td class=\"text-start\">PacBio Sequel IIe</td>\n                </tr>\n                <tr>\n                    <td class=\"text-center\">M</td>\n                    <td class=\"text-start\">Ultima Genomics UG 100</td>\n                </tr>\n                <tr>\n                    <td class=\"cell-small-text text-start\">(set the codes as data are generated on different sequencing platforms and submitted to DAC)</td>\n                    <td class=\"text-start\">PacBio Onso</td>\n                </tr>\n            </tbody>\n        </table>\n    </div>\n\n\n\nTable 3B. Experimental assay codes.\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n.. raw:: html\n\n    <div class=\"table-responsive\">\n        <table class=\"table table-sm text-start\">\n            <thead class=\"thead-smaht table-borderless\">\n                <tr>\n                    <th>Code</th>\n                    <th>Assay Name</th>\n                    <th>Description</th>\n                </tr>\n            </thead>\n            <tbody class=\"table-border-inner\">\n                <tr>\n                    <td>000</td>\n                    <td></td>\n                    <td>(Null or not-applicable)</td>\n                </tr>\n                <tr class=\"table-stripe-secondary text-600 fst-italic\">\n                    <td colspan=\"3\">[001-100: DNA-based assays]</td>\n                </tr>\n                <tr>\n                    <td>001</td>\n                    <td>WGS</td>\n                    <td>DNA, PCR-free, Bulk, Whole genome sequencing (WGS)</td>\n                </tr>\n                <tr>\n                    <td>002</td>\n                    <td>PCR WGS</td>\n                    <td>DNA PCR, Bulk, WGS</td>\n                </tr>\n                <tr>\n                    <td>003</td>\n                    <td>Ultra-Long WGS</td>\n                    <td>DNA, PCR-free, Bulk, Ultra-Long WGS</td>\n                </tr>\n                <tr>\n                    <td>004</td>\n                    <td>Fiber-seq</td>\n                    <td>DNA, PCR-free, Bulk, Fiber-seq</td>\n                </tr>\n                <tr>\n                    <td>005</td>\n                    <td>Hi-C</td>\n                    <td>DNA, Bulk, Hi-C</td>\n                </tr>\n                <tr>\n                    <td>006</td>\n                    <td>Bulk NTSeq</td>\n                    <td>DNA, Bulk, NTSeq</td>\n                </tr>\n                <tr>\n                    <td>007</td>\n                    <td>CODEC</td>\n                    <td>DNA, Bulk, Duplex-seq, CODEC</td>\n                </tr>\n                <tr>\n                    <td>008</td>\n                    <td>Bot-seq</td>\n                    <td>DNA, Bulk, Duplex-seq, Bot-seq</td>\n                </tr>\n                <tr>\n                    <td>009</td>\n                    <td>NanoSeq</td>\n                    <td>DNA, Bulk, Duplex-seq, NanoSeq</td>\n                </tr>\n                <tr>\n                    <td>010</td>\n                    <td>scNanoSeq</td>\n                    <td>DNA, Single-cell, Duplex-seq, scNanoSeq</td>\n                </tr>\n                <tr>\n                    <td>011</td>\n                    <td>DLP+</td>\n                    <td>DNA, Single-cell, DLP+</td>\n                </tr>\n                <tr>\n                    <td>012</td>\n                    <td>Microbulk MALBAC WGS</td>\n                    <td>DNA, Microbulk, MALBAC-amplified WGS</td>\n                </tr>\n                <tr>\n                    <td>013</td>\n                    <td>Single-cell MALBAC WGS</td>\n                    <td>DNA, Single-cell, MALBAC-amplified WGS</td>\n                </tr>\n                <tr>\n                    <td>014</td>\n                    <td>Microbulk PTA WGS</td>\n                    <td>DNA, Microbulk, PTA-amplified WGS</td>\n                </tr>\n                <tr>\n                    <td>015</td>\n                    <td>Single-cell PTA WGS</td>\n                    <td>DNA, Single-cell, PTA-amplified WGS</td>\n                </tr>\n                <tr>\n                    <td>016</td>\n                    <td>scDip-C</td>\n                    <td>DNA, Single-cell, scDip-C</td>\n                </tr>\n                <tr>\n                    <td>017</td>\n                    <td>CompDuplex-seq</td>\n                    <td>DNA, Bulk, Duplex-seq, CompDuplex-seq</td>\n                </tr>\n                <tr>\n                    <td>018</td>\n                    <td>scCompDuplex-seq</td>\n                    <td>DNA, Single-cell, Duplex-seq, scCompDuplex-seq</td>\n                </tr>\n                <tr>\n                    <td>019</td>\n                    <td>Strand-seq</td>\n                    <td>DNA, Bulk, Strand-seq</td>\n                </tr>\n                <tr>\n                    <td>020</td>\n                    <td>scStrand-seq</td>\n                    <td>DNA, Single-cell, scStrand-seq</td>\n                </tr>\n                <tr>\n                    <td>021</td>\n                    <td>HiDEF-seq</td>\n                    <td>DNA, Bulk, Duplex-seq, HiDEF-seq</td>\n                </tr>\n                <tr>\n                    <td>022</td>\n                    <td>HAT-seq</td>\n                    <td>DNA, Bulk, HAT-seq</td>\n                </tr>\n                <tr>\n                    <td>023</td>\n                    <td>Microbulk HAT-seq</td>\n                    <td>DNA, Microbulk, PTA-amplified HAT-seq</td>\n                </tr>\n                <tr>\n                    <td>024</td>\n                    <td>scHAT-seq</td>\n                    <td>DNA, Single-cell, PTA-amplified, HAT-seq</td>\n                </tr>\n                <tr>\n                    <td>025</td>\n                    <td>VISTA-seq</td>\n                    <td>DNA, Bulk, Duplex-seq, VISTA-seq</td>\n                </tr>\n                <tr>\n                    <td>026</td>\n                    <td>Microbulk VISTA-seq</td>\n                    <td>DNA, Microbulk, Duplex-seq, VISTA-seq</td>\n                </tr>\n                <tr>\n                    <td>027</td>\n                    <td>scVISTA-seq</td>\n                    <td>DNA, Single-cell, Duplex-seq, VISTA-seq</td>\n                </tr>\n                <tr>\n                    <td>028</td>\n                    <td>TEnCATS</td>\n                    <td>DNA, Bulk, TEnCATS</td>\n                </tr>\n                <tr>\n                    <td>029</td>\n                    <td>L1-ONT</td>\n                    <td>DNA, Bulk, L1-ONT</td>\n                </tr>\n                <tr>\n                    <td>030</td>\n                    <td>ppmSeq</td>\n                    <td>DNA, Bulk, Duplex-seq, ppmSeq</td>\n                </tr>\n                <tr>\n                    <td colspan=\"3\" class=\"pb-3 pt-07\"></td>\n                </tr>\n                <tr class=\"table-stripe-secondary fst-italic text-600\">\n                    <td colspan=\"3\">[101-200: RNA-based assays]</td>\n                </tr>\n                <tr>\n                    <td>101</td>\n                    <td>RNA-seq</td>\n                    <td>RNA, Bulk, RNA-seq</td>\n                </tr>\n                <tr>\n                    <td>102</td>\n                    <td>Kinnex</td>\n                    <td>RNA, Bulk, Kinnex</td>\n                </tr>\n                <tr>\n                    <td>103</td>\n                    <td>snRNA-seq</td>\n                    <td>RNA, Single-cell, snRNA-seq</td>\n                </tr>\n                <tr>\n                    <td>104</td>\n                    <td>STORM-Seq</td>\n                    <td>RNA, Single-cell, STORM-seq</td>\n                </tr>\n                <tr>\n                    <td>105</td>\n                    <td>Tranquil-Seq</td>\n                    <td>RNA, Single-cell, Tranquil-seq</td>\n                </tr>\n                <tr>\n                    <td colspan=\"3\" class=\"pb-3 pt-07\"></td>\n                </tr>\n                <tr class=\"table-stripe-secondary fst-italic text-600\">\n                    <td colspan=\"3\">[201-300: Chromatin-based assays]</td>\n                </tr>\n                <tr>\n                    <td>201</td>\n                    <td>ATAC-seq</td>\n                    <td>Chromatin, Bulk, ATAC-seq</td>\n                </tr>\n                <tr>\n                    <td>202</td>\n                    <td>CUT&Tag</td>\n                    <td>Chromatin, Bulk, CUT&Tag</td>\n                </tr>\n                <tr>\n                    <td>203</td>\n                    <td>varCUT&Tag</td>\n                    <td>Chromatin, Bulk, varCUT&Tag</td>\n                </tr>\n                <tr>\n                    <td>204</td>\n                    <td>sc-varCUT&Tag</td>\n                    <td>Chromatin, Single-cell, sc-varCUT&Tag</td>\n                </tr>\n                <tr>\n                    <td colspan=\"3\" class=\"pb-3 pt-07\"></td>\n                </tr>\n            </tbody>\n        </table>\n    </div>\n\n\nTable 4. SMaHT data generation center codes.\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n.. raw:: html\n\n    <div class=\"table-responsive\">\n        <table class=\"table table-striped table-sm text-start\">\n            <thead class=\"thead-smaht table-borderless\">\n                <tr>\n                    <th>Code</th>\n                    <th>Category</th>\n                    <th>Institute</th>\n                    <th>Contact PI</th>\n                </tr>\n            </thead>\n            <tbody class=\"table-border-inner\">\n                <tr>\n                    <td>bcm</td>\n                    <td>GCC</td>\n                    <td>Baylor College of Medicine</td>\n                    <td>Richard Gibbs</td>\n                </tr>\n                <tr>\n                    <td>broad</td>\n                    <td>GCC</td>\n                    <td>Broad Institute</td>\n                    <td>Kristin Ardlie</td>\n                </tr>\n                <tr>\n                    <td>nygc</td>\n                    <td>GCC</td>\n                    <td>New York Genome Center</td>\n                    <td>Soren Germer</td>\n                </tr>\n                <tr>\n                    <td>uwsc</td>\n                    <td>GCC</td>\n                    <td>University of Washington & Seattle Children\u2019s Hospital</td>\n                    <td>Jimmy Bennett</td>\n                </tr>\n                <tr>\n                    <td>washu</td>\n                    <td>GCC</td>\n                    <td>Washington University in St. Louis</td>\n                    <td>Ting Wang</td>\n                </tr>\n                <tr>\n                    <td>bcm1</td>\n                    <td>TTD</td>\n                    <td>Baylor College of Medicine</td>\n                    <td>Chuck Zong</td>\n                </tr>\n                <tr>\n                    <td>bcm2</td>\n                    <td>TTD</td>\n                    <td>Baylor College of Medicine</td>\n                    <td>Fritz Sedlazeck</td>\n                </tr>\n                <tr>\n                    <td>bch1</td>\n                    <td>TTD</td>\n                    <td>Boston Children\u2019s Hospital</td>\n                    <td>Christopher Walsh</td>\n                </tr>\n                <tr>\n                    <td>bch2</td>\n                    <td>TTD</td>\n                    <td>Boston Children\u2019s Hospital</td>\n                    <td>Sangita Choudhury</td>\n                </tr>\n                <tr>\n                    <td>broad1</td>\n                    <td>TTD</td>\n                    <td>Broad Institute</td>\n                    <td>Fei Chen</td>\n                </tr>\n                <tr>\n                    <td>cwru</td>\n                    <td>TTD</td>\n                    <td>Case Western Reserve University</td>\n                    <td>Fulai Jin</td>\n                </tr>\n                <tr>\n                    <td>dfci</td>\n                    <td>TTD</td>\n                    <td>Dana-Farber Cancer Institute</td>\n                    <td>Kathleen Burns</td>\n                </tr>\n                <tr>\n                    <td>mayo</td>\n                    <td>TTD</td>\n                    <td>Mayo Clinic</td>\n                    <td>Alexej Arbyzov</td>\n                </tr>\n                <tr>\n                    <td>nyu</td>\n                    <td>TTD</td>\n                    <td>New York University</td>\n                    <td>Gilad Evrony</td>\n                </tr>\n                <tr>\n                    <td>stfd</td>\n                    <td>TTD</td>\n                    <td>Stanford University</td>\n                    <td>Alexander Urban</td>\n                </tr>\n                <tr>\n                    <td>umass</td>\n                    <td>TTD</td>\n                    <td>University of Massachusetts</td>\n                    <td>Thomas Fazzio</td>\n                </tr>\n                <tr>\n                    <td>umich</td>\n                    <td>TTD</td>\n                    <td>University of Michigan</td>\n                    <td>Ryan Mills</td>\n                </tr>\n                <tr>\n                    <td>uutah</td>\n                    <td>TTD</td>\n                    <td>University of Utah</td>\n                    <td>Gabor Marth</td>\n                </tr>\n                <tr>\n                    <td>wcnygc</td>\n                    <td>TTD</td>\n                    <td>Weill Cornell Medicine & New York Genome Center</td>\n                    <td>Dan Landau</td>\n                </tr>\n                <tr>\n                    <td>dac</td>\n                    <td>DAC</td>\n                    <td>Harvard Medical School</td>\n                    <td>Peter Park</td>\n                </tr>\n                <tr>\n                    <td>tpc</td>\n                    <td>TPC</td>\n                    <td>National Disease Research Interchange (NDRI)</td>\n                    <td>Thomas Bell</td>\n                </tr>\n            </tbody>\n        </table>\n    </div>\n\n\nPart 3: File Name breakdown\n---------------------------\n\n.. raw:: html\n\n    <img class=\"grey-border\" src=\"/static/img/Nomenclature_Part3.png\" alt=\"Nomenclature Part 3\"/>\n\n\nTable 5. Genome version (A) and variant type (B) tables.\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n.. raw:: html\n\n    <div class=\"table-responsive\">\n        <table class=\"table table-sm text-start\">\n            <caption style=\"caption-side:top;\">(A)</caption>\n            <thead class=\"thead-smaht table-borderless\">\n                <tr>\n                    <th>Reference Genome</th>\n                    <th>Code</th>\n                </tr>\n            </thead>\n            <tbody class=\"table-border-inner\">\n                <tr>\n                    <td>GRCh38 without ALT contigs</td>\n                    <td>GRCh38</td>\n                </tr>\n                <tr>\n                    <td>GRCh38 with ALT contigs</td>\n                    <td>GRCh38_ALT</td>\n                </tr>\n                <tr>\n                    <td>T2T CHM13</td>\n                    <td>CHM13</td>\n                </tr>\n                <tr>\n                    <td>Donor-specific genome assembly</td>\n                    <td>DSA</td>\n                </tr>\n            </tbody>\n        </table>\n        <table class=\"table table-sm text-start\">\n            <caption style=\"caption-side:top;\">(B)</caption>\n            <thead class=\"thead-smaht table-borderless\">\n                <tr>\n                    <th>Data Type</th>\n                    <th>Code</th>\n                </tr>\n            </thead>\n            <tbody class=\"table-border-inner\">\n                <tr>\n                    <td>Reference conversion</td>\n                    <td>[Source]To[Target]</td>\n                </tr>\n                <tr>\n                    <td>Donor-specific genome assembly haplotype</td>\n                    <td>hapX, hapY, hapX1, hapX2</td>\n                </tr>\n                <tr>\n                    <td>Gene expression level</td>\n                    <td>gene</td>\n                </tr>\n                <tr>\n                    <td>Transcript isoform expression level or isoform information</td>\n                    <td>isoform</td>\n                </tr>\n                <tr>\n                    <td>Junction annotations</td>\n                    <td>junction</td>\n                </tr>\n                <tr>\n                    <td>Full-length, non-concatemer (FLNC) Kinnex reads</td>\n                    <td>flnc</td>\n                </tr>\n                <tr>\n                    <td>Aligned consensus Duplex-Seq BAM</td>\n                    <td>consensus</td>\n                </tr>\n            </tbody>\n        </table>\n    </div>\n\n\nExample Files with the SMaHT Nomenclature\n-----------------------------------------\n\n.. raw:: html\n\n    <img class=\"grey-border\" src=\"/static/img/Nomenclature_ExampleFiles.png\" alt=\"Nomenclature_ExampleFiles\"/>\n\n", "filetype": "rst"}], "consortia": [{"status": "open", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "@type": ["Consortium", "Item"], "display_title": 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