{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7172AAET/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7172AAET",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR1_S38",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR2_S44",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR3_S134",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR4_S140"
],
"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 [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/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8103DFGV](/in-vitro-systems/IGVFSM8103DFGV/) 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/IGVFSM8103DFGV/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7172AAET](/measurement-sets/IGVFDS7172AAET/) 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/IGVFDS7172AAET/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7172AAET](/measurement-sets/IGVFDS7172AAET/) has sequence file(s) [IGVFFI2912TQBY](/sequence-files/IGVFFI2912TQBY/), [IGVFFI3317MYOR](/sequence-files/IGVFFI3317MYOR/), [IGVFFI1472FMGU](/sequence-files/IGVFFI1472FMGU/), [IGVFFI1580YHAZ](/sequence-files/IGVFFI1580YHAZ/) 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/IGVFDS7172AAET/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8103DFGV](/in-vitro-systems/IGVFSM8103DFGV/) 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/IGVFSM8103DFGV/"
}
]
},
"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": "2024-05-16T17:33:43.939556+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/IGVFFI4617WKOB/",
"accession": "IGVFFI4617WKOB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR2_S44"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:37.589808+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI4617WKOB/@@download/IGVFFI4617WKOB.yaml.gz",
"md5sum": "12ffe433a1263efefced3ab849905c8c",
"s3_uri": "s3://igvf-files/2024/06/11/df8751c0-6e77-4c39-9892-34f347abf1d9/IGVFFI4617WKOB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinB-PCR2_S44.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6811ZTYV/",
"accession": "IGVFFI6811ZTYV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR1_S38"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:24.402801+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI6811ZTYV/@@download/IGVFFI6811ZTYV.yaml.gz",
"md5sum": "0d6fafb3271d1181a1de37d9c4489160",
"s3_uri": "s3://igvf-files/2024/06/11/c95c0af6-b1c7-4c17-8369-95b64227c77f/IGVFFI6811ZTYV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinB-PCR1_S38.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3523GZOA/",
"accession": "IGVFFI3523GZOA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR3_S134"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:51.961030+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI3523GZOA/@@download/IGVFFI3523GZOA.yaml.gz",
"md5sum": "be43654f897d793aa477556e9b2bae9e",
"s3_uri": "s3://igvf-files/2024/06/11/ed1701da-6c63-43d2-a9a8-e8dfe9f7cbd1/IGVFFI3523GZOA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinB-PCR3_S134.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI2912TQBY/",
"accession": "IGVFFI2912TQBY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR4_S140"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:39.522252+00:00",
"file_format": "fastq",
"file_size": 13126213,
"href": "/sequence-files/IGVFFI2912TQBY/@@download/IGVFFI2912TQBY.fastq.gz",
"md5sum": "48a145b6e5b83a688b43d3c33bcb2501",
"s3_uri": "s3://igvf-files/2024/06/01/2a775039-c232-4305-8232-261d49902cfd/IGVFFI2912TQBY.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-BinB-PCR4_S140_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4252HVDY/",
"accession": "IGVFFI4252HVDY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR4_S140"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:06.340621+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI4252HVDY/@@download/IGVFFI4252HVDY.yaml.gz",
"md5sum": "6d2cff2b3f2a4a7f17e26eb120b731bc",
"s3_uri": "s3://igvf-files/2024/06/11/f14686bc-5469-491f-b642-062b6c511aa8/IGVFFI4252HVDY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinB-PCR4_S140.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3317MYOR/",
"accession": "IGVFFI3317MYOR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR1_S38"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:43.878501+00:00",
"file_format": "fastq",
"file_size": 6932229,
"href": "/sequence-files/IGVFFI3317MYOR/@@download/IGVFFI3317MYOR.fastq.gz",
"md5sum": "7c25acf5763cad6906681024dd05f12c",
"s3_uri": "s3://igvf-files/2024/06/01/d9638422-c8a6-468b-8b4a-a809e8f3dc9e/IGVFFI3317MYOR.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-BinB-PCR1_S38_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1472FMGU/",
"accession": "IGVFFI1472FMGU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR3_S134"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:20.963825+00:00",
"file_format": "fastq",
"file_size": 14790613,
"href": "/sequence-files/IGVFFI1472FMGU/@@download/IGVFFI1472FMGU.fastq.gz",
"md5sum": "ffaf928d5c4a46655da816a3a28b5cde",
"s3_uri": "s3://igvf-files/2024/06/01/828ff8b1-be77-4d6c-a7dd-301efe640b09/IGVFFI1472FMGU.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-BinB-PCR3_S134_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1580YHAZ/",
"accession": "IGVFFI1580YHAZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR2_S44"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:19:02.098966+00:00",
"file_format": "fastq",
"file_size": 6790441,
"href": "/sequence-files/IGVFFI1580YHAZ/@@download/IGVFFI1580YHAZ.fastq.gz",
"md5sum": "864a009e38a88d012a19a84fe73818b3",
"s3_uri": "s3://igvf-files/2024/06/01/849209ba-b1da-4e7d-8651-400fd71b66e6/IGVFFI1580YHAZ.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-BinB-PCR2_S44_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": "2024-07-10T19:43:38.186752+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8103DFGV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8103DFGV",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR1_S38",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR2_S44",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR3_S134",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinB-PCR4_S140"
],
"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 B for 10-20% 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": "2024-06-01T02:18:43.878501+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": "9f7a987c-a889-4a80-b2b1-d3c79e10dade"
}