{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8112FQWI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8112FQWI",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR1_S76",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR2_S172",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR3_S268",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR4_S364"
],
"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 [IGVFSM4919VWFX](/in-vitro-systems/IGVFSM4919VWFX/) 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/IGVFSM4919VWFX/"
},
{
"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 [IGVFDS8112FQWI](/measurement-sets/IGVFDS8112FQWI/) 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/IGVFDS8112FQWI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8112FQWI](/measurement-sets/IGVFDS8112FQWI/) has sequence file(s) [IGVFFI1203ZTZE](/sequence-files/IGVFFI1203ZTZE/), [IGVFFI6571KHFQ](/sequence-files/IGVFFI6571KHFQ/), [IGVFFI1476GXSD](/sequence-files/IGVFFI1476GXSD/), [IGVFFI5165MIAB](/sequence-files/IGVFFI5165MIAB/) 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/IGVFDS8112FQWI/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM4919VWFX](/in-vitro-systems/IGVFSM4919VWFX/) 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/IGVFSM4919VWFX/"
}
]
},
"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": "2024-05-06T22:19:34.064493+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/IGVFFI9163IOAI/",
"accession": "IGVFFI9163IOAI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR2_S172"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:08.138543+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI9163IOAI/@@download/IGVFFI9163IOAI.yaml.gz",
"md5sum": "81c4bd0754f97ab15aac11f23587e0bd",
"s3_uri": "s3://igvf-files/2024/06/11/0ee2e090-4742-4a81-aff1-a2a5f52db533/IGVFFI9163IOAI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinD-PCR2_S172.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9147CEGC/",
"accession": "IGVFFI9147CEGC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR1_S76"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:54.908223+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI9147CEGC/@@download/IGVFFI9147CEGC.yaml.gz",
"md5sum": "75bd44cc7f4cc5c96517eba70aff94ab",
"s3_uri": "s3://igvf-files/2024/06/11/ab7edbe3-fdda-42b5-ae3c-aed90300f41a/IGVFFI9147CEGC.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinD-PCR1_S76.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4546XKME/",
"accession": "IGVFFI4546XKME",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR4_S364"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:34.525454+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI4546XKME/@@download/IGVFFI4546XKME.yaml.gz",
"md5sum": "4df880d8a30e4a8b554d5beb27003657",
"s3_uri": "s3://igvf-files/2024/06/11/2d63afc8-71b3-4d56-a3b3-c1e0e6f92dcc/IGVFFI4546XKME.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinD-PCR4_S364.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1203ZTZE/",
"accession": "IGVFFI1203ZTZE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR1_S76"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:20.124232+00:00",
"file_format": "fastq",
"file_size": 7385980,
"href": "/sequence-files/IGVFFI1203ZTZE/@@download/IGVFFI1203ZTZE.fastq.gz",
"md5sum": "7a9425695c6785d0ea1fa7bdc0977145",
"s3_uri": "s3://igvf-files/2024/06/01/5581497c-3073-47e7-abfc-f0e83c00c9f9/IGVFFI1203ZTZE.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-BinD-PCR1_S76_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6571KHFQ/",
"accession": "IGVFFI6571KHFQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR2_S172"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:35.991187+00:00",
"file_format": "fastq",
"file_size": 7492292,
"href": "/sequence-files/IGVFFI6571KHFQ/@@download/IGVFFI6571KHFQ.fastq.gz",
"md5sum": "9e8d845d5abaa3d1e6450ee848b1b17e",
"s3_uri": "s3://igvf-files/2024/06/01/32e569b0-484b-4ba1-8cd3-b5f232cf80c2/IGVFFI6571KHFQ.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-BinD-PCR2_S172_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1476GXSD/",
"accession": "IGVFFI1476GXSD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR3_S268"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:52.248393+00:00",
"file_format": "fastq",
"file_size": 10208424,
"href": "/sequence-files/IGVFFI1476GXSD/@@download/IGVFFI1476GXSD.fastq.gz",
"md5sum": "99b6d556a5b5294aeb4ae58015036a65",
"s3_uri": "s3://igvf-files/2024/06/01/5d9fc373-62b1-44e6-82a2-d62b31e5d393/IGVFFI1476GXSD.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-BinD-PCR3_S268_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1645EINR/",
"accession": "IGVFFI1645EINR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR3_S268"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:21.298400+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI1645EINR/@@download/IGVFFI1645EINR.yaml.gz",
"md5sum": "4d86f4230d48b931c88c99eb47b63e55",
"s3_uri": "s3://igvf-files/2024/06/11/4a0c6ab0-ee02-465b-a782-adcaea913753/IGVFFI1645EINR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinD-PCR3_S268.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5165MIAB/",
"accession": "IGVFFI5165MIAB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR4_S364"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:30:08.787178+00:00",
"file_format": "fastq",
"file_size": 10078674,
"href": "/sequence-files/IGVFFI5165MIAB/@@download/IGVFFI5165MIAB.fastq.gz",
"md5sum": "85d9ed5908ba00ef968d6de9cefbbdbb",
"s3_uri": "s3://igvf-files/2024/06/01/d269dc55-ec35-4403-8919-5db1c90f9ee7/IGVFFI5165MIAB.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-BinD-PCR4_S364_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": "2024-07-10T19:49:34.209799+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4919VWFX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4919VWFX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR1_S76",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR2_S172",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR3_S268",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinD-PCR4_S364"
],
"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 D for 55-65% 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": "2024-06-01T01:29:20.124232+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": "860f3022-df81-408b-96cd-0b09a06ddb2d"
}