{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8391VNJE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8391VNJE",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86"
],
"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 [IGVFSM8531AKQD](/in-vitro-systems/IGVFSM8531AKQD/) 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/IGVFSM8531AKQD/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS6020CDHF](/auxiliary-sets/IGVFDS6020CDHF/) 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/IGVFDS6020CDHF/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8391VNJE](/measurement-sets/IGVFDS8391VNJE/) 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/IGVFDS8391VNJE/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8391VNJE](/measurement-sets/IGVFDS8391VNJE/) has sequence file(s) [IGVFFI9364JMZY](/sequence-files/IGVFFI9364JMZY/), [IGVFFI9695GFTP](/sequence-files/IGVFFI9695GFTP/), [IGVFFI1079QGZM](/sequence-files/IGVFFI1079QGZM/), [IGVFFI1233TQNL](/sequence-files/IGVFFI1233TQNL/) 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/IGVFDS8391VNJE/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8531AKQD](/in-vitro-systems/IGVFSM8531AKQD/) 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/IGVFSM8531AKQD/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6020CDHF/",
"accession": "IGVFDS6020CDHF",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_SSFA2-Auxin6hrs-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/IGVFDS5413RKIA/",
"accession": "IGVFDS5413RKIA",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5130EWUZ/",
"accession": "IGVFFI5130EWUZ",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-05-14T20:54:39.880161+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/IGVFFI6904JXET/",
"accession": "IGVFFI6904JXET",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:16.606923+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI6904JXET/@@download/IGVFFI6904JXET.yaml.gz",
"md5sum": "e7dd41b49aa25ee0c3bfc0620348865f",
"s3_uri": "s3://igvf-files/2024/06/11/e227e839-c8da-41ab-9fd9-d2cef8c5e599/IGVFFI6904JXET.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0605XPPL/",
"accession": "IGVFFI0605XPPL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:31.748189+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI0605XPPL/@@download/IGVFFI0605XPPL.yaml.gz",
"md5sum": "a744469b7d42543c47963c0a1db9cdb9",
"s3_uri": "s3://igvf-files/2024/06/11/d9f26d35-b2b5-4c74-a224-f45eebcb6add/IGVFFI0605XPPL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2269TFRI/",
"accession": "IGVFFI2269TFRI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:45.714418+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2269TFRI/@@download/IGVFFI2269TFRI.yaml.gz",
"md5sum": "857d4e99b754cefd3bc2abab04092468",
"s3_uri": "s3://igvf-files/2024/06/11/1c21485b-12d1-4d34-8181-38b47f9368c2/IGVFFI2269TFRI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9364JMZY/",
"accession": "IGVFFI9364JMZY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:44.581782+00:00",
"file_format": "fastq",
"file_size": 22861403,
"href": "/sequence-files/IGVFFI9364JMZY/@@download/IGVFFI9364JMZY.fastq.gz",
"md5sum": "7ab75a01439951748ab28d370e92cd48",
"s3_uri": "s3://igvf-files/2024/06/01/59df6e18-feac-45d2-b253-b34965bb49e2/IGVFFI9364JMZY.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/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9695GFTP/",
"accession": "IGVFFI9695GFTP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:02.808912+00:00",
"file_format": "fastq",
"file_size": 20227298,
"href": "/sequence-files/IGVFFI9695GFTP/@@download/IGVFFI9695GFTP.fastq.gz",
"md5sum": "c2b379f9a03784f085bd2a19067d94d1",
"s3_uri": "s3://igvf-files/2024/06/01/f9517372-73a1-4e75-9185-3a763b8402ef/IGVFFI9695GFTP.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/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4536MNTO/",
"accession": "IGVFFI4536MNTO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:01.343958+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4536MNTO/@@download/IGVFFI4536MNTO.yaml.gz",
"md5sum": "74381eefa2da01ff1186a9fd7b959e10",
"s3_uri": "s3://igvf-files/2024/06/11/d1094865-0bf7-406a-a199-d08bafcc0bdb/IGVFFI4536MNTO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1079QGZM/",
"accession": "IGVFFI1079QGZM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:26.364604+00:00",
"file_format": "fastq",
"file_size": 12234670,
"href": "/sequence-files/IGVFFI1079QGZM/@@download/IGVFFI1079QGZM.fastq.gz",
"md5sum": "5f71ec38b884353890cc3b413a73d4ec",
"s3_uri": "s3://igvf-files/2024/06/01/e26863d5-01fd-4713-b850-0582512bbfaf/IGVFFI1079QGZM.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/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1233TQNL/",
"accession": "IGVFFI1233TQNL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:08.052605+00:00",
"file_format": "fastq",
"file_size": 11893852,
"href": "/sequence-files/IGVFFI1233TQNL/@@download/IGVFFI1233TQNL.fastq.gz",
"md5sum": "115a99efa2550256843f7700545839f9",
"s3_uri": "s3://igvf-files/2024/06/01/30e720e3-cdd9-48c6-8e95-ae25ba9966b2/IGVFFI1233TQNL.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/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2031CTSP/"
],
"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": "2024-07-10T19:52:11.893800+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8531AKQD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8531AKQD",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR1-Rep1_S26",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR2-Rep1_S32",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR3-Rep1_S80",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinB-PCR4-Rep1_S86"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"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 B for 10-20% expression of SSFA2) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:47:08.052605+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of ITPRID2 integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000138434/",
"geneid": "ENSG00000138434",
"name": "ITPR interacting domain containing 2",
"status": "released",
"symbol": "ITPRID2",
"synonyms": [
"sperm associated antigen 13",
"ITPR interacting domain containing 2",
"ITPR-interacting domain-containing protein 2",
"SSFA2",
"KRAS-induced actin-interacting protein",
"cleavage signal-1 protein",
"ki-ras-induced actin-interacting protein",
"sperm specific antigen 2",
"ITPRID2",
"SPAG13",
"protein ITPRID2",
"CS-1",
"CS1",
"KRAP"
]
}
],
"uuid": "a8566eb0-cc56-48c8-9c91-32da0f2b4d2e"
}