{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1681VDMR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1681VDMR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR1_S37",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR2_S43",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR3_S133",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR4_S139"
],
"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 [IGVFSM1476GCQU](/in-vitro-systems/IGVFSM1476GCQU/) 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/IGVFSM1476GCQU/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1681VDMR](/measurement-sets/IGVFDS1681VDMR/) 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/IGVFDS1681VDMR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1681VDMR](/measurement-sets/IGVFDS1681VDMR/) has sequence file(s) [IGVFFI7682XDAF](/sequence-files/IGVFFI7682XDAF/), [IGVFFI3780QMCR](/sequence-files/IGVFFI3780QMCR/), [IGVFFI8017EEHN](/sequence-files/IGVFFI8017EEHN/), [IGVFFI1299YDLA](/sequence-files/IGVFFI1299YDLA/) 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/IGVFDS1681VDMR/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS4590CBRM](/auxiliary-sets/IGVFDS4590CBRM/) 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/IGVFDS4590CBRM/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM1476GCQU](/in-vitro-systems/IGVFSM1476GCQU/) 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/IGVFSM1476GCQU/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4590CBRM/",
"accession": "IGVFDS4590CBRM",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin0hrs-FF4"
],
"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/IGVFDS7846UISG/",
"accession": "IGVFDS7846UISG",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5995VHKI/",
"accession": "IGVFFI5995VHKI",
"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": "2024-05-16T17:33:43.073316+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/IGVFFI9850DZDZ/",
"accession": "IGVFFI9850DZDZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR2_S43"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:35.351205+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI9850DZDZ/@@download/IGVFFI9850DZDZ.yaml.gz",
"md5sum": "3607ecb0759279e9bad26c02625132f8",
"s3_uri": "s3://igvf-files/2024/06/11/cd0cab8e-0cc9-47c0-bf02-85b08a4ece58/IGVFFI9850DZDZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinA-PCR2_S43.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6476ZXDT/",
"accession": "IGVFFI6476ZXDT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR3_S133"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:49.527632+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI6476ZXDT/@@download/IGVFFI6476ZXDT.yaml.gz",
"md5sum": "46892f68be85516ca53d4e46814ae10a",
"s3_uri": "s3://igvf-files/2024/06/11/d5c134bf-1eab-47ce-827e-236e2698a3e1/IGVFFI6476ZXDT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinA-PCR3_S133.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9458GGZZ/",
"accession": "IGVFFI9458GGZZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR4_S139"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:03.898587+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI9458GGZZ/@@download/IGVFFI9458GGZZ.yaml.gz",
"md5sum": "96f9aa09f0d9127dbf07ebed5b300e1f",
"s3_uri": "s3://igvf-files/2024/06/11/758b4238-9ba5-46b3-9f78-230a5937c247/IGVFFI9458GGZZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinA-PCR4_S139.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7682XDAF/",
"accession": "IGVFFI7682XDAF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR1_S37"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:40.906870+00:00",
"file_format": "fastq",
"file_size": 11269013,
"href": "/sequence-files/IGVFFI7682XDAF/@@download/IGVFFI7682XDAF.fastq.gz",
"md5sum": "f93b41e11150dd28f7b3e48efc7e1187",
"s3_uri": "s3://igvf-files/2024/06/01/27d19971-49e6-4137-93d3-77a7d7e8b376/IGVFFI7682XDAF.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/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinA-PCR1_S37_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3780QMCR/",
"accession": "IGVFFI3780QMCR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR3_S133"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:18.070838+00:00",
"file_format": "fastq",
"file_size": 23790861,
"href": "/sequence-files/IGVFFI3780QMCR/@@download/IGVFFI3780QMCR.fastq.gz",
"md5sum": "4bdfcf700c79790dd28f14ac4f898f84",
"s3_uri": "s3://igvf-files/2024/06/01/b0425bfe-1c32-4b92-aaab-a28e2d29d63b/IGVFFI3780QMCR.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/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinA-PCR3_S133_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8017EEHN/",
"accession": "IGVFFI8017EEHN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR4_S139"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:36.424657+00:00",
"file_format": "fastq",
"file_size": 19687583,
"href": "/sequence-files/IGVFFI8017EEHN/@@download/IGVFFI8017EEHN.fastq.gz",
"md5sum": "a57dc8903e31aaad91d5e3bbec1f14f6",
"s3_uri": "s3://igvf-files/2024/06/01/45c8401c-2bf5-4016-9d88-f13e531bc10c/IGVFFI8017EEHN.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/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinA-PCR4_S139_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9566VEHX/",
"accession": "IGVFFI9566VEHX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR1_S37"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:22.127329+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI9566VEHX/@@download/IGVFFI9566VEHX.yaml.gz",
"md5sum": "00903c80bf7b8a57137901d7742a5e7f",
"s3_uri": "s3://igvf-files/2024/06/11/ef9acef7-a87b-4286-bede-afb97cbedd03/IGVFFI9566VEHX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinA-PCR1_S37.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1299YDLA/",
"accession": "IGVFFI1299YDLA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR2_S43"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:59.016448+00:00",
"file_format": "fastq",
"file_size": 11266830,
"href": "/sequence-files/IGVFFI1299YDLA/@@download/IGVFFI1299YDLA.fastq.gz",
"md5sum": "edcabb4a5eeb80709c851e50e622e4a9",
"s3_uri": "s3://igvf-files/2024/06/01/1ca406a2-e58d-489b-bd81-7f2fb3996757/IGVFFI1299YDLA.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/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinA-PCR2_S43_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"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": "2024-07-10T19:43:32.768575+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1476GCQU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1476GCQU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR1_S37",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR2_S43",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR3_S133",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR4_S139"
],
"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 KITLG) 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": "2024-06-01T02:18:40.906870+00:00",
"summary": " CRISPR FlowFISH screen sorted on the expression of KITLG integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000049130/",
"geneid": "ENSG00000049130",
"name": "KIT ligand",
"status": "released",
"symbol": "KITLG",
"synonyms": [
"SF",
"WS2F",
"Kitl",
"FPH2",
"SCF",
"KL-1",
"DFNA69",
"familial progressive hyperpigmentation 2",
"mast cell growth factor",
"DCUA",
"kit ligand",
"c-Kit ligand",
"SLF",
"steel factor",
"KITLG",
"SHEP7",
"stem cell factor",
"KIT ligand",
"FPHH",
"MGF"
]
}
],
"uuid": "4927e371-f3f3-4989-b449-127bf0ef6877"
}