{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3741DKGN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3741DKGN",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR1_S77",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR2_S173",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR3_S269",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR4_S365"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1617PVUY](/in-vitro-systems/IGVFSM1617PVUY/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM1617PVUY/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS5292OCBC](/auxiliary-sets/IGVFDS5292OCBC/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/auxiliary-sets/IGVFDS5292OCBC/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3741DKGN](/measurement-sets/IGVFDS3741DKGN/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS3741DKGN/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3741DKGN](/measurement-sets/IGVFDS3741DKGN/) has sequence file(s) [IGVFFI5740TOCS](/sequence-files/IGVFFI5740TOCS/), [IGVFFI0509HCWG](/sequence-files/IGVFFI0509HCWG/), [IGVFFI2718BNTR](/sequence-files/IGVFFI2718BNTR/), [IGVFFI1351KSFG](/sequence-files/IGVFFI1351KSFG/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS3741DKGN/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM1617PVUY](/in-vitro-systems/IGVFSM1617PVUY/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM1617PVUY/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5292OCBC/",
"accession": "IGVFDS5292OCBC",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_PILOT_CCND1-Auxin0hrs-FF1"
],
"file_set_type": "cell sorting",
"status": "released"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0392OWNZ/",
"accession": "IGVFDS0392OWNZ",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI4981YFMT/",
"accession": "IGVFFI4981YFMT",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in 36 genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-05-06T22:19:34.956171+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"documents": [
"/documents/74d53b9c-ab1d-42e3-b679-d3a00ae3d842/"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI0038OXWJ/",
"accession": "IGVFFI0038OXWJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR4_S365"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:36.938742+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI0038OXWJ/@@download/IGVFFI0038OXWJ.yaml.gz",
"md5sum": "8a7db35f464336707e12df31178ad118",
"s3_uri": "s3://igvf-files/2024/06/11/ea1e9f0e-0883-4430-90b5-95f5b3389f49/IGVFFI0038OXWJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinE-PCR4_S365.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5740TOCS/",
"accession": "IGVFFI5740TOCS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR2_S173"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:38.615861+00:00",
"file_format": "fastq",
"file_size": 7503769,
"href": "/sequence-files/IGVFFI5740TOCS/@@download/IGVFFI5740TOCS.fastq.gz",
"md5sum": "cabc29e334f0c1e8f36e08be68a1e7e1",
"s3_uri": "s3://igvf-files/2024/06/01/edec47c4-e919-4374-8f4b-40d2585ec691/IGVFFI5740TOCS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinE-PCR2_S173_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4005IDLG/",
"accession": "IGVFFI4005IDLG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR1_S77"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:57.199207+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI4005IDLG/@@download/IGVFFI4005IDLG.yaml.gz",
"md5sum": "aa943b1100d72c2568c996e6f5f48e87",
"s3_uri": "s3://igvf-files/2024/06/11/b2776d0c-1ad2-4350-9685-dc5445b9ba1a/IGVFFI4005IDLG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinE-PCR1_S77.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8761WVJE/",
"accession": "IGVFFI8761WVJE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR2_S173"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:10.288107+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI8761WVJE/@@download/IGVFFI8761WVJE.yaml.gz",
"md5sum": "d895c67bb5d6567df2e117ba007b7cbe",
"s3_uri": "s3://igvf-files/2024/06/11/70e60d0a-2f91-436f-a5e0-32d88872d303/IGVFFI8761WVJE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinE-PCR2_S173.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2623ANUZ/",
"accession": "IGVFFI2623ANUZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR3_S269"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:23.564092+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI2623ANUZ/@@download/IGVFFI2623ANUZ.yaml.gz",
"md5sum": "01b14c1ace242b1c4ff59426264f0203",
"s3_uri": "s3://igvf-files/2024/06/11/7bbfe4fc-1d54-4fa1-97fb-7551aa0911c8/IGVFFI2623ANUZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinE-PCR3_S269.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0509HCWG/",
"accession": "IGVFFI0509HCWG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR3_S269"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:55.335598+00:00",
"file_format": "fastq",
"file_size": 10826442,
"href": "/sequence-files/IGVFFI0509HCWG/@@download/IGVFFI0509HCWG.fastq.gz",
"md5sum": "f7e7cc0fa215ca87482e8bbf48edeb4f",
"s3_uri": "s3://igvf-files/2024/06/01/c61ad7e2-59fb-40c7-96e8-31672ee5802a/IGVFFI0509HCWG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinE-PCR3_S269_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2718BNTR/",
"accession": "IGVFFI2718BNTR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR4_S365"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:30:11.668951+00:00",
"file_format": "fastq",
"file_size": 9102960,
"href": "/sequence-files/IGVFFI2718BNTR/@@download/IGVFFI2718BNTR.fastq.gz",
"md5sum": "159dd5919a830b47552820f53d9c7b6f",
"s3_uri": "s3://igvf-files/2024/06/01/1ed45f62-a741-4e93-8ea7-802cb300a387/IGVFFI2718BNTR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinE-PCR4_S365_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1351KSFG/",
"accession": "IGVFFI1351KSFG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR1_S77"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:22.856337+00:00",
"file_format": "fastq",
"file_size": 5621093,
"href": "/sequence-files/IGVFFI1351KSFG/@@download/IGVFFI1351KSFG.fastq.gz",
"md5sum": "6d9f6021e61698a045ea104f55db013b",
"s3_uri": "s3://igvf-files/2024/06/01/3ef076da-aadd-4d3f-89d0-648feaf8dc00/IGVFFI1351KSFG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinE-PCR1_S77_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2982SJGW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:49:41.573065+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1617PVUY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1617PVUY",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR1_S77",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR2_S173",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR3_S269",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinE-PCR4_S365"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin E for 80-90% expression of CCND1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:29:22.856337+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of CCND1 integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000110092/",
"geneid": "ENSG00000110092",
"name": "cyclin D1",
"status": "released",
"symbol": "CCND1",
"synonyms": [
"U21B31",
"cyclin D1",
"B-cell CLL/lymphoma 1",
"PRAD1 oncogene",
"PRAD1",
"CCND1",
"G1/S-specific cyclin-D1",
"BCL-1 oncogene",
"BCL1",
"D11S287E",
"B-cell lymphoma 1 protein"
]
}
],
"uuid": "4713076d-a512-4e00-821d-bfcf0e8240b1"
}