{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9498BKLC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9498BKLC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR1_S29",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR2_S35",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR3_S125",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR4_S131"
],
"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 [IGVFDS0329USVJ](/auxiliary-sets/IGVFDS0329USVJ/) 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/IGVFDS0329USVJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0596STHT](/in-vitro-systems/IGVFSM0596STHT/) 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/IGVFSM0596STHT/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9498BKLC](/measurement-sets/IGVFDS9498BKLC/) 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/IGVFDS9498BKLC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9498BKLC](/measurement-sets/IGVFDS9498BKLC/) has sequence file(s) [IGVFFI7056URWW](/sequence-files/IGVFFI7056URWW/), [IGVFFI4420MMWA](/sequence-files/IGVFFI4420MMWA/), [IGVFFI1262UZWR](/sequence-files/IGVFFI1262UZWR/), [IGVFFI8116SREE](/sequence-files/IGVFFI8116SREE/) 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/IGVFDS9498BKLC/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM0596STHT](/in-vitro-systems/IGVFSM0596STHT/) 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/IGVFSM0596STHT/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0329USVJ/",
"accession": "IGVFDS0329USVJ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin0hrs-FF3"
],
"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": "2024-05-16T17:33:22.980843+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/IGVFFI1263XHMB/",
"accession": "IGVFFI1263XHMB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR4_S131"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:17.780766+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1263XHMB/@@download/IGVFFI1263XHMB.yaml.gz",
"md5sum": "08570623c448ca7761e4f37fea5fbda6",
"s3_uri": "s3://igvf-files/2024/06/11/52380662-eca1-4964-9ed8-ced9bd4a5e8d/IGVFFI1263XHMB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinE-PCR4_S131.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6946JJKZ/",
"accession": "IGVFFI6946JJKZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR3_S125"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:04.499774+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI6946JJKZ/@@download/IGVFFI6946JJKZ.yaml.gz",
"md5sum": "2687faa8160a807f1d90ee262faf1faf",
"s3_uri": "s3://igvf-files/2024/06/11/1e15d39a-523f-46d2-b2ff-f3b42b83ab44/IGVFFI6946JJKZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinE-PCR3_S125.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7018BVOW/",
"accession": "IGVFFI7018BVOW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR2_S35"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:51.305025+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI7018BVOW/@@download/IGVFFI7018BVOW.yaml.gz",
"md5sum": "0713392ee8843206137eba611ff8906e",
"s3_uri": "s3://igvf-files/2024/06/11/d904a362-5731-40d9-b340-a7e456df80cb/IGVFFI7018BVOW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinE-PCR2_S35.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1204XAGV/",
"accession": "IGVFFI1204XAGV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR1_S29"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:38.167567+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI1204XAGV/@@download/IGVFFI1204XAGV.yaml.gz",
"md5sum": "f22af59099978bdcf8a782885fee1686",
"s3_uri": "s3://igvf-files/2024/06/11/e882493e-903c-4908-8696-f468aaa17851/IGVFFI1204XAGV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinE-PCR1_S29.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7056URWW/",
"accession": "IGVFFI7056URWW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR3_S125"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:12.720454+00:00",
"file_format": "fastq",
"file_size": 15620018,
"href": "/sequence-files/IGVFFI7056URWW/@@download/IGVFFI7056URWW.fastq.gz",
"md5sum": "149991d87a07f59137168d8238334e3d",
"s3_uri": "s3://igvf-files/2024/06/01/24bfb3dc-36eb-4a7f-a124-67cb9b7d66f2/IGVFFI7056URWW.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-FF3-BinE-PCR3_S125_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4420MMWA/",
"accession": "IGVFFI4420MMWA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR2_S35"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:54.767308+00:00",
"file_format": "fastq",
"file_size": 12422630,
"href": "/sequence-files/IGVFFI4420MMWA/@@download/IGVFFI4420MMWA.fastq.gz",
"md5sum": "f658bd1559dd07d269187baeccd18519",
"s3_uri": "s3://igvf-files/2024/06/01/82c96975-e983-4f43-8c1b-78ec9ad54732/IGVFFI4420MMWA.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-FF3-BinE-PCR2_S35_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1262UZWR/",
"accession": "IGVFFI1262UZWR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR1_S29"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:36.651541+00:00",
"file_format": "fastq",
"file_size": 8054235,
"href": "/sequence-files/IGVFFI1262UZWR/@@download/IGVFFI1262UZWR.fastq.gz",
"md5sum": "b93f720de5df6b844b35019469da7a8b",
"s3_uri": "s3://igvf-files/2024/06/01/14a6f507-a79c-45b3-95de-705ad09e624b/IGVFFI1262UZWR.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-FF3-BinE-PCR1_S29_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8116SREE/",
"accession": "IGVFFI8116SREE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR4_S131"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:31.280501+00:00",
"file_format": "fastq",
"file_size": 20036420,
"href": "/sequence-files/IGVFFI8116SREE/@@download/IGVFFI8116SREE.fastq.gz",
"md5sum": "987c533166d2ccd0190c39e03d0594ac",
"s3_uri": "s3://igvf-files/2024/06/01/b0f9a0f9-20b5-4732-9f12-c76124d298ba/IGVFFI8116SREE.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-FF3-BinE-PCR4_S131_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": "2024-07-10T19:43:22.464239+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0596STHT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0596STHT",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR1_S29",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR2_S35",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR3_S125",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinE-PCR4_S131"
],
"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 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": "2024-06-01T02:17:36.651541+00:00",
"summary": "mixed 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": "71bab714-f4ee-4e9e-81b4-69aad3799094"
}