{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4021XJLW/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4021XJLW",
"aliases": [
"jay-shendure:analysis_set_CRISPRa_ipscNeurons"
],
"assay_titles": [
"scCRISPR screen"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI8270PCLP](/matrix-files/IGVFFI8270PCLP/) 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/IGVFFI8270PCLP/"
},
{
"category": "missing reference files",
"detail": "Analysis set [IGVFDS4021XJLW](/analysis-sets/IGVFDS4021XJLW/) has file(s) with no transcriptome `reference_files`: [IGVFFI8270PCLP](/matrix-files/IGVFFI8270PCLP/) 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/IGVFDS4021XJLW/"
}
],
"WARNING": [
{
"category": "unexpected workflows",
"detail": "Analysis set [IGVFDS4021XJLW](/analysis-sets/IGVFDS4021XJLW/) has multiple `workflows` linked to its files: [IGVFFI8270PCLP](/matrix-files/IGVFFI8270PCLP/) link(s) to [IGVFWF7562QXLM](/workflows/IGVFWF7562QXLM/), [IGVFFI9048CVLI](/tabular-files/IGVFFI9048CVLI/), [IGVFFI4846IRZK](/tabular-files/IGVFFI4846IRZK/) 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/IGVFDS4021XJLW/"
}
]
},
"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": "2023-12-12T23:07:35.141749+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI8270PCLP/",
"accession": "IGVFFI8270PCLP",
"aliases": [
"jay-shendure:analysis_set_CRISPRa_ipscNeurons_matrix"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2023-12-13T00:09:58.340992+00:00",
"file_format": "tar",
"file_size": 441930008,
"href": "/matrix-files/IGVFFI8270PCLP/@@download/IGVFFI8270PCLP.tar.gz",
"s3_uri": "s3://igvf-files/2023/12/13/543c9f4e-1511-4167-8a5b-843c99af20b3/IGVFFI8270PCLP.tar.gz",
"status": "released",
"submitted_file_name": "/net/shendure/vol10/projects/IGVFtemp/Shendure_IpscNeurons_CRISPRa_matrix.tar.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI9048CVLI/",
"accession": "IGVFFI9048CVLI",
"aliases": [
"jay-shendure:tabularfile_S7_Chardon-McDiarmid"
],
"content_type": "differential gene expression quantifications",
"controlled_access": false,
"creation_timestamp": "2024-10-14T18:39:01.617294+00:00",
"file_format": "csv",
"file_size": 2012,
"href": "/tabular-files/IGVFFI9048CVLI/@@download/IGVFFI9048CVLI.csv.gz",
"s3_uri": "s3://igvf-files/2024/10/14/8d65544d-405c-4fa3-91f8-2fcaa3be20e1/IGVFFI9048CVLI.csv.gz",
"status": "released",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/CRISPRa/41467_2024_52490_MOESM10_ESM.csv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4846IRZK/",
"accession": "IGVFFI4846IRZK",
"aliases": [
"jay-shendure:tabularfile_S14_Chardon-McDiarmid"
],
"content_type": "differential gene expression quantifications",
"controlled_access": false,
"creation_timestamp": "2024-10-14T18:39:05.424482+00:00",
"file_format": "csv",
"file_size": 1732,
"href": "/tabular-files/IGVFFI4846IRZK/@@download/IGVFFI4846IRZK.csv.gz",
"s3_uri": "s3://igvf-files/2024/10/14/b3b5abba-927b-4a72-aa4a-a827d2ddff32/IGVFFI4846IRZK.csv.gz",
"status": "released",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/CRISPRa/41467_2024_52490_MOESM17_ESM.csv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS9384BVGM/",
"accession": "IGVFDS9384BVGM",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane1_exprs"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0272VVTX/",
"accession": "IGVFDS0272VVTX",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane2_exprs"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2385QENN/",
"accession": "IGVFDS2385QENN",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane3_exprs"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2133JAFB/",
"accession": "IGVFDS2133JAFB",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane4_exprs"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS8386FNRJ/",
"accession": "IGVFDS8386FNRJ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane1_CS1"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS2220HHTN/",
"accession": "IGVFDS2220HHTN",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane2_CS1"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS2532AVSC/",
"accession": "IGVFDS2532AVSC",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane3_CS1"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS7598WPXV/",
"accession": "IGVFDS7598WPXV",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane4_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": "2024-08-13T20:47:19.906363+00:00",
"sample_summary": "Homo sapiens GM25256 (WTC-11) differentiated cell specimen induced to neuron, at 19 day(s) post change, modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7750SNNY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7750SNNY",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane1"
],
"cellular_sub_pool": "10Xlane1",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane1) modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"status": "released",
"term_name": "neuron"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM8382KOXO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8382KOXO",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane4"
],
"cellular_sub_pool": "10Xlane4",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane4) modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"status": "released",
"term_name": "neuron"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM8317ZTFV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8317ZTFV",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane3"
],
"cellular_sub_pool": "10Xlane3",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane3) modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"status": "released",
"term_name": "neuron"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM9913PXTT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9913PXTT",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane2"
],
"cellular_sub_pool": "10Xlane2",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane2) modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"status": "released",
"term_name": "neuron"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-13T00:09:58.340992+00:00",
"summary": "scCRISPR activation screen: differential gene expression quantifications, filtered feature barcode matrix",
"uuid": "c54949f6-6673-4a8e-a213-5cb972f23dea",
"workflows": [
{
"@id": "/workflows/IGVFWF1905PJEA/",
"accession": "IGVFWF1905PJEA",
"name": "Shendure scCRISPRa Pipeline",
"status": "released",
"uniform_pipeline": false
},
{
"@id": "/workflows/IGVFWF7562QXLM/",
"accession": "IGVFWF7562QXLM",
"name": "Cell Ranger Gene Count Pipeline",
"status": "released"
}
]
}