{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9183CPVF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9183CPVF",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR1_S90",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR2_S96",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR3_S186",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR4_S192"
],
"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 [IGVFDS0877LMZO](/auxiliary-sets/IGVFDS0877LMZO/) 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/IGVFDS0877LMZO/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1655HPGH](/in-vitro-systems/IGVFSM1655HPGH/) 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/IGVFSM1655HPGH/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9183CPVF](/measurement-sets/IGVFDS9183CPVF/) 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/IGVFDS9183CPVF/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9183CPVF](/measurement-sets/IGVFDS9183CPVF/) has sequence file(s) [IGVFFI4429ZJPV](/sequence-files/IGVFFI4429ZJPV/), [IGVFFI0227JJOM](/sequence-files/IGVFFI0227JJOM/), [IGVFFI9673DFOR](/sequence-files/IGVFFI9673DFOR/), [IGVFFI8610SEGJ](/sequence-files/IGVFFI8610SEGJ/) 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/IGVFDS9183CPVF/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM1655HPGH](/in-vitro-systems/IGVFSM1655HPGH/) 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/IGVFSM1655HPGH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0877LMZO/",
"accession": "IGVFDS0877LMZO",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin6hrs-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": "2024-05-16T17:57:46.285672+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/IGVFFI2753RZSU/",
"accession": "IGVFFI2753RZSU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR2_S96"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:44.032171+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2753RZSU/@@download/IGVFFI2753RZSU.yaml.gz",
"md5sum": "65a2b62d043dc9e848df02b0c726f9f5",
"s3_uri": "s3://igvf-files/2024/06/11/ee5b09d1-7e70-4f22-b6aa-72f01da0320f/IGVFFI2753RZSU.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinF-PCR2_S96.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2020ZSYY/",
"accession": "IGVFFI2020ZSYY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR1_S90"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:29.153459+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2020ZSYY/@@download/IGVFFI2020ZSYY.yaml.gz",
"md5sum": "6d123201b3e27b85ae7fc9467ba30a1f",
"s3_uri": "s3://igvf-files/2024/06/11/8a034352-bf70-4994-bc3d-4b9b04f581e8/IGVFFI2020ZSYY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinF-PCR1_S90.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4429ZJPV/",
"accession": "IGVFFI4429ZJPV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR4_S192"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:54.040158+00:00",
"file_format": "fastq",
"file_size": 20726500,
"href": "/sequence-files/IGVFFI4429ZJPV/@@download/IGVFFI4429ZJPV.fastq.gz",
"md5sum": "bf013f5bc54283b13ff70fe4cf3969cb",
"s3_uri": "s3://igvf-files/2024/06/03/e62c92b5-6515-43f5-9efa-dd5a3b233648/IGVFFI4429ZJPV.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/Auxin6hrs-FF4-BinF-PCR4_S192_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1208IBPS/",
"accession": "IGVFFI1208IBPS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR4_S192"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:13:13.298182+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI1208IBPS/@@download/IGVFFI1208IBPS.yaml.gz",
"md5sum": "1b44f29985ed069b4c09a5d4c9f76c97",
"s3_uri": "s3://igvf-files/2024/06/11/ee6e2ae8-3df0-4465-b01e-92188e5602b8/IGVFFI1208IBPS.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinF-PCR4_S192.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4600EVHN/",
"accession": "IGVFFI4600EVHN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR3_S186"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:58.548861+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI4600EVHN/@@download/IGVFFI4600EVHN.yaml.gz",
"md5sum": "030f0f824ce7c4c11ffc4142274a881c",
"s3_uri": "s3://igvf-files/2024/06/11/d33d0314-b457-4b89-9dd7-cd1eda56ddf8/IGVFFI4600EVHN.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinF-PCR3_S186.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0227JJOM/",
"accession": "IGVFFI0227JJOM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR1_S90"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:04.494504+00:00",
"file_format": "fastq",
"file_size": 4872644,
"href": "/sequence-files/IGVFFI0227JJOM/@@download/IGVFFI0227JJOM.fastq.gz",
"md5sum": "b682e2ca65f2495a3017b1e2225692c9",
"s3_uri": "s3://igvf-files/2024/06/03/ebdbb1e7-ad48-41ec-965c-71f399afc726/IGVFFI0227JJOM.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/Auxin6hrs-FF4-BinF-PCR1_S90_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9673DFOR/",
"accession": "IGVFFI9673DFOR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR2_S96"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:20.522798+00:00",
"file_format": "fastq",
"file_size": 3890654,
"href": "/sequence-files/IGVFFI9673DFOR/@@download/IGVFFI9673DFOR.fastq.gz",
"md5sum": "90c87306802937b9c503a2c3a69659e9",
"s3_uri": "s3://igvf-files/2024/06/03/a38d2320-9db1-4174-82d5-260d1cb66315/IGVFFI9673DFOR.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/Auxin6hrs-FF4-BinF-PCR2_S96_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8610SEGJ/",
"accession": "IGVFFI8610SEGJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR3_S186"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:37.414938+00:00",
"file_format": "fastq",
"file_size": 6631250,
"href": "/sequence-files/IGVFFI8610SEGJ/@@download/IGVFFI8610SEGJ.fastq.gz",
"md5sum": "681bd1d31f39d1e9a877461890a32bae",
"s3_uri": "s3://igvf-files/2024/06/03/99121842-3ed4-46cb-b378-3469e037f3df/IGVFFI8610SEGJ.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/Auxin6hrs-FF4-BinF-PCR3_S186_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": "2024-07-10T19:46:11.226579+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1655HPGH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1655HPGH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR1_S90",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR2_S96",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR3_S186",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinF-PCR4_S192"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"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 F for 80-100% expression of KITLG) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-03T15:28:04.494504+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": "5bb10134-e247-4192-8d64-4f6df99f3bc1"
}