{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8123YLWP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8123YLWP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR1_S73",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR2_S169",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR3_S265",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR4_S361"
],
"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": "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": "In vitro system [IGVFSM7865RIGH](/in-vitro-systems/IGVFSM7865RIGH/) 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/IGVFSM7865RIGH/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8123YLWP](/measurement-sets/IGVFDS8123YLWP/) 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/IGVFDS8123YLWP/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8123YLWP](/measurement-sets/IGVFDS8123YLWP/) has sequence file(s) [IGVFFI3567ECNQ](/sequence-files/IGVFFI3567ECNQ/), [IGVFFI1597PAXC](/sequence-files/IGVFFI1597PAXC/), [IGVFFI1611MQSG](/sequence-files/IGVFFI1611MQSG/), [IGVFFI1011WVNT](/sequence-files/IGVFFI1011WVNT/) 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/IGVFDS8123YLWP/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7865RIGH](/in-vitro-systems/IGVFSM7865RIGH/) 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/IGVFSM7865RIGH/"
}
]
},
"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": "2024-05-06T22:19:31.325925+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/IGVFFI0209ENJY/",
"accession": "IGVFFI0209ENJY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR3_S265"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:14.747347+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI0209ENJY/@@download/IGVFFI0209ENJY.yaml.gz",
"md5sum": "8521a723bc5050dc1cafdd4ae91254c2",
"s3_uri": "s3://igvf-files/2024/06/11/638ec703-0ae4-460f-8a1b-f1d586da8af4/IGVFFI0209ENJY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinA-PCR3_S265.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1582BSGK/",
"accession": "IGVFFI1582BSGK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR4_S361"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:28.078052+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI1582BSGK/@@download/IGVFFI1582BSGK.yaml.gz",
"md5sum": "f04ca2c935f0aced3dc5caaca45e98f7",
"s3_uri": "s3://igvf-files/2024/06/11/397e6f90-9c82-4364-b260-ff02a7e57f2a/IGVFFI1582BSGK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinA-PCR4_S361.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4517BOFT/",
"accession": "IGVFFI4517BOFT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR1_S73"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:48.446439+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI4517BOFT/@@download/IGVFFI4517BOFT.yaml.gz",
"md5sum": "6a3b46bee70909a9b7fae1876486a519",
"s3_uri": "s3://igvf-files/2024/06/11/5e5de2f3-5174-47ef-a522-67147b924ad6/IGVFFI4517BOFT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinA-PCR1_S73.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3567ECNQ/",
"accession": "IGVFFI3567ECNQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR1_S73"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:12.448220+00:00",
"file_format": "fastq",
"file_size": 3768611,
"href": "/sequence-files/IGVFFI3567ECNQ/@@download/IGVFFI3567ECNQ.fastq.gz",
"md5sum": "15a2e70a2b2c8d54bc469d7711cf055a",
"s3_uri": "s3://igvf-files/2024/06/01/24cd9a75-f0e0-450d-a39b-f5550616214c/IGVFFI3567ECNQ.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-BinA-PCR1_S73_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4133KBSX/",
"accession": "IGVFFI4133KBSX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR2_S169"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:01.442311+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI4133KBSX/@@download/IGVFFI4133KBSX.yaml.gz",
"md5sum": "96fef769039d506b2ef23f6f3720097e",
"s3_uri": "s3://igvf-files/2024/06/11/07649c01-c324-4d8d-b87e-f1cd3e7a54a5/IGVFFI4133KBSX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinA-PCR2_S169.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1597PAXC/",
"accession": "IGVFFI1597PAXC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR4_S361"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:30:00.738447+00:00",
"file_format": "fastq",
"file_size": 7325011,
"href": "/sequence-files/IGVFFI1597PAXC/@@download/IGVFFI1597PAXC.fastq.gz",
"md5sum": "9e1625adae029a0b3687ff1a5f2137ff",
"s3_uri": "s3://igvf-files/2024/06/01/777a051b-b55f-4f2e-a8f2-71e179eb1d5e/IGVFFI1597PAXC.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-BinA-PCR4_S361_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1611MQSG/",
"accession": "IGVFFI1611MQSG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR2_S169"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:28.134153+00:00",
"file_format": "fastq",
"file_size": 7306295,
"href": "/sequence-files/IGVFFI1611MQSG/@@download/IGVFFI1611MQSG.fastq.gz",
"md5sum": "651c63294e078c65801e797249612e86",
"s3_uri": "s3://igvf-files/2024/06/01/6e48eefb-f6c8-4ea4-988f-f4a6275b7b68/IGVFFI1611MQSG.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-BinA-PCR2_S169_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1011WVNT/",
"accession": "IGVFFI1011WVNT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR3_S265"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:43.806818+00:00",
"file_format": "fastq",
"file_size": 6368053,
"href": "/sequence-files/IGVFFI1011WVNT/@@download/IGVFFI1011WVNT.fastq.gz",
"md5sum": "8ddc8cbfaf07ba8533cccabac44ab21a",
"s3_uri": "s3://igvf-files/2024/06/01/81c7a41d-1da3-4cfd-b17e-4fcef475e62a/IGVFFI1011WVNT.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-BinA-PCR3_S265_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": "2024-07-10T19:49:12.992172+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7865RIGH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7865RIGH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR1_S73",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR2_S169",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR3_S265",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinA-PCR4_S361"
],
"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 A for 0-10% 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": "2024-06-01T01:29:12.448220+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": "3478c7ed-2786-40d4-9ef1-d37b5059e17c"
}