{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS9078ZWQH/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9078ZWQH",
"aliases": [
"jay-shendure:analysis_set_CRISPRa_K562"
],
"assay_titles": [
"scCRISPR screen"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing reference files",
"detail": "Analysis set [IGVFDS9078ZWQH](/analysis-sets/IGVFDS9078ZWQH/) has file(s) with no transcriptome `reference_files`: [IGVFFI5731ZKRJ](/matrix-files/IGVFFI5731ZKRJ/) Analysis set files processed from transcript sequence data are expected to link to a transcriptome reference.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_transcriptome",
"path": "/analysis-sets/IGVFDS9078ZWQH/"
},
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI5731ZKRJ](/matrix-files/IGVFFI5731ZKRJ/) has no `file_format_specifications`. Matrix files are expected to link to a file format specifications document describing the axes and layers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_file_no_file_format_specifications",
"path": "/matrix-files/IGVFFI5731ZKRJ/"
}
],
"WARNING": [
{
"category": "unexpected workflows",
"detail": "Analysis set [IGVFDS9078ZWQH](/analysis-sets/IGVFDS9078ZWQH/) has multiple `workflows` linked to its files: [IGVFFI5731ZKRJ](/matrix-files/IGVFFI5731ZKRJ/) link(s) to [IGVFWF7562QXLM](/workflows/IGVFWF7562QXLM/), [IGVFFI5652WMRK](/tabular-files/IGVFFI5652WMRK/), [IGVFFI4612KEHH](/tabular-files/IGVFFI4612KEHH/) link(s) to [IGVFWF1905PJEA](/workflows/IGVFWF1905PJEA/). Analysis sets are not expected to link to more than one workflow.",
"level": 40,
"level_name": "WARNING",
"name": "audit_analysis_set_multiple_workflows",
"path": "/analysis-sets/IGVFDS9078ZWQH/"
}
]
},
"award": {
"@id": "/awards/HG011966/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/eb543cda-67b7-493c-84eb-187d0dac13ba/",
"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7581DNXF/",
"accession": "IGVFDS7581DNXF",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI2463QNJD/",
"accession": "IGVFFI2463QNJD",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2023-12-12T23:07:33.755844+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI5731ZKRJ/",
"accession": "IGVFFI5731ZKRJ",
"aliases": [
"jay-shendure:analysis_set_CRISPRa_K562_matrix"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2023-12-13T00:09:56.255569+00:00",
"file_format": "tar",
"file_size": 537616943,
"href": "/matrix-files/IGVFFI5731ZKRJ/@@download/IGVFFI5731ZKRJ.tar.gz",
"s3_uri": "s3://igvf-files/2023/12/13/f6f37514-eaf7-4b5d-97b9-e00a37f3ac1d/IGVFFI5731ZKRJ.tar.gz",
"status": "released",
"submitted_file_name": "/net/shendure/vol10/projects/IGVFtemp/Shendure_K562_CRISPRa_matrix.tar.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI5652WMRK/",
"accession": "IGVFFI5652WMRK",
"aliases": [
"jay-shendure:tabularfile_S4_Chardon-McDiarmid"
],
"content_type": "differential gene expression quantifications",
"controlled_access": false,
"creation_timestamp": "2024-10-14T18:38:59.978827+00:00",
"file_format": "csv",
"file_size": 6873,
"href": "/tabular-files/IGVFFI5652WMRK/@@download/IGVFFI5652WMRK.csv.gz",
"s3_uri": "s3://igvf-files/2024/10/14/9b9c5715-ed24-42c5-b663-ae7424ee582d/IGVFFI5652WMRK.csv.gz",
"status": "released",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/CRISPRa/41467_2024_52490_MOESM7_ESM.csv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4612KEHH/",
"accession": "IGVFFI4612KEHH",
"aliases": [
"jay-shendure:tabularfile_S11_Chardon-McDiarmid"
],
"content_type": "differential gene expression quantifications",
"controlled_access": false,
"creation_timestamp": "2024-10-14T18:39:03.562166+00:00",
"file_format": "csv",
"file_size": 3314,
"href": "/tabular-files/IGVFFI4612KEHH/@@download/IGVFFI4612KEHH.csv.gz",
"s3_uri": "s3://igvf-files/2024/10/14/12aa9f23-4832-4e9e-9cc2-9d94f4545063/IGVFFI4612KEHH.csv.gz",
"status": "released",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/CRISPRa/41467_2024_52490_MOESM14_ESM.csv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4863BMGZ/",
"accession": "IGVFDS4863BMGZ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane1_exprs"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8535CXVX/",
"accession": "IGVFDS8535CXVX",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane2_exprs"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7395DPAD/",
"accession": "IGVFDS7395DPAD",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane1_exprs"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0508ERUQ/",
"accession": "IGVFDS0508ERUQ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane2_exprs"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS4502LQQH/",
"accession": "IGVFDS4502LQQH",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane1_CS1"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS8929VNCP/",
"accession": "IGVFDS8929VNCP",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane2_CS1"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS4621HUKP/",
"accession": "IGVFDS4621HUKP",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane1_CS1"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS4834SKZS/",
"accession": "IGVFDS4834SKZS",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane2_CS1"
],
"file_set_type": "gRNA sequencing",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"notes": "This object's file_set_type was primary analysis and has been updated to be principal analysis.",
"protocols": [
"https://www.protocols.io/view/methods-from-multiplex-single-cell-crispra-screeni-c5zvy766"
],
"publications": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1038/s41467-024-52490-4"
],
"status": "released"
}
],
"release_timestamp": "2024-08-13T20:47:06.196314+00:00",
"sample_summary": "Homo sapiens K562 cell line, modified with CRISPRa Sp-dCas9-VP64, CRISPRa Sp-dCas9-VP64-p65-Rta (VPR), transfected with a guide library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9390JSDH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9390JSDH",
"aliases": [
"jay-shendure:CRISPRa_VP64_K562_10Xlane2"
],
"cellular_sub_pool": "10Xlane2",
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line (cellular sub pool: 10Xlane2) modified with CRISPRa Sp-dCas9-VP64, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM9542NUGS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9542NUGS",
"aliases": [
"jay-shendure:CRISPRa_VPR_K562_10Xlane2"
],
"cellular_sub_pool": "10Xlane2",
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/8b61bce4-105c-435e-9b32-1c8903566a9b/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line (cellular sub pool: 10Xlane2) modified with CRISPRa Sp-dCas9-VP64-p65-Rta (VPR), transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM4521QSSO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4521QSSO",
"aliases": [
"jay-shendure:CRISPRa_VP64_K562_10Xlane1"
],
"cellular_sub_pool": "10Xlane1",
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line (cellular sub pool: 10Xlane1) modified with CRISPRa Sp-dCas9-VP64, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM1594ZOQH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1594ZOQH",
"aliases": [
"jay-shendure:CRISPRa_VPR_K562_10Xlane1"
],
"cellular_sub_pool": "10Xlane1",
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/8b61bce4-105c-435e-9b32-1c8903566a9b/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line (cellular sub pool: 10Xlane1) modified with CRISPRa Sp-dCas9-VP64-p65-Rta (VPR), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-13T00:09:56.255569+00:00",
"summary": "scCRISPR activation screen: differential gene expression quantifications, filtered feature barcode matrix",
"uuid": "5257dd49-492f-49b1-88fd-8b812ae8c188",
"workflows": [
{
"@id": "/workflows/IGVFWF7562QXLM/",
"accession": "IGVFWF7562QXLM",
"name": "Cell Ranger Gene Count Pipeline",
"status": "released"
},
{
"@id": "/workflows/IGVFWF1905PJEA/",
"accession": "IGVFWF1905PJEA",
"name": "Shendure scCRISPRa Pipeline",
"status": "released",
"uniform_pipeline": false
}
]
}