{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2761VFZT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2761VFZT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR1_S76",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR2_S82",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR3_S172",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR4_S178"
],
"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": "Measurement set [IGVFDS2761VFZT](/measurement-sets/IGVFDS2761VFZT/) 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/IGVFDS2761VFZT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2761VFZT](/measurement-sets/IGVFDS2761VFZT/) has sequence file(s) [IGVFFI9570QMSC](/sequence-files/IGVFFI9570QMSC/), [IGVFFI0845BJAV](/sequence-files/IGVFFI0845BJAV/), [IGVFFI0083XVCI](/sequence-files/IGVFFI0083XVCI/), [IGVFFI4284VDSK](/sequence-files/IGVFFI4284VDSK/) 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/IGVFDS2761VFZT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9423PKNV](/in-vitro-systems/IGVFSM9423PKNV/) 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/IGVFSM9423PKNV/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS7947IZNE](/auxiliary-sets/IGVFDS7947IZNE/) 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/IGVFDS7947IZNE/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9423PKNV](/in-vitro-systems/IGVFSM9423PKNV/) 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/IGVFSM9423PKNV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7947IZNE/",
"accession": "IGVFDS7947IZNE",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin6hrs-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": "2024-05-16T17:57:20.987960+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/IGVFFI8096DLBK/",
"accession": "IGVFFI8096DLBK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR4_S178"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:10.090536+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI8096DLBK/@@download/IGVFFI8096DLBK.yaml.gz",
"md5sum": "c9033a0bc8392c675dc3cd7c49c17f4a",
"s3_uri": "s3://igvf-files/2024/06/11/2756f847-6684-4cfb-9e45-a4fa63c74346/IGVFFI8096DLBK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinD-PCR4_S178.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9462XNHY/",
"accession": "IGVFFI9462XNHY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR1_S76"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:26.443852+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI9462XNHY/@@download/IGVFFI9462XNHY.yaml.gz",
"md5sum": "416c3d6984e581fdc2df8f8805e47a87",
"s3_uri": "s3://igvf-files/2024/06/11/b5f2077d-39aa-4fd6-b84c-80450f3247a9/IGVFFI9462XNHY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinD-PCR1_S76.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4045XHTX/",
"accession": "IGVFFI4045XHTX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR3_S172"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:55.851754+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI4045XHTX/@@download/IGVFFI4045XHTX.yaml.gz",
"md5sum": "6285d3494c11a8ed47c4c12188daf8e2",
"s3_uri": "s3://igvf-files/2024/06/11/e7852e89-8fe5-4ecf-8646-1c80e263763d/IGVFFI4045XHTX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinD-PCR3_S172.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2378YWGY/",
"accession": "IGVFFI2378YWGY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR2_S82"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:40.934979+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2378YWGY/@@download/IGVFFI2378YWGY.yaml.gz",
"md5sum": "17fd098e038386f4716542e51d701600",
"s3_uri": "s3://igvf-files/2024/06/11/b55e4a83-3a6c-4ec8-9a32-8916983b9ffd/IGVFFI2378YWGY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF3-BinD-PCR2_S82.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9570QMSC/",
"accession": "IGVFFI9570QMSC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR2_S82"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:09.124247+00:00",
"file_format": "fastq",
"file_size": 6288848,
"href": "/sequence-files/IGVFFI9570QMSC/@@download/IGVFFI9570QMSC.fastq.gz",
"md5sum": "b16a73e7c4051332f978368a6c5e772d",
"s3_uri": "s3://igvf-files/2024/06/03/ca00503f-1cf1-486a-b24b-c3598ea66c30/IGVFFI9570QMSC.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-FF3-BinD-PCR2_S82_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0845BJAV/",
"accession": "IGVFFI0845BJAV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR1_S76"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:26:53.207664+00:00",
"file_format": "fastq",
"file_size": 10056509,
"href": "/sequence-files/IGVFFI0845BJAV/@@download/IGVFFI0845BJAV.fastq.gz",
"md5sum": "62e6b7ef542283399e9aec65a0f79194",
"s3_uri": "s3://igvf-files/2024/06/03/3d1c01a1-f2d9-47d5-ab07-cbbfa19face2/IGVFFI0845BJAV.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-FF3-BinD-PCR1_S76_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0083XVCI/",
"accession": "IGVFFI0083XVCI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR4_S178"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:42.529488+00:00",
"file_format": "fastq",
"file_size": 13997526,
"href": "/sequence-files/IGVFFI0083XVCI/@@download/IGVFFI0083XVCI.fastq.gz",
"md5sum": "e233096b43dd34ee13e0a01edca95fdf",
"s3_uri": "s3://igvf-files/2024/06/03/35f77d53-aad8-4b18-9ef4-ceca8572da35/IGVFFI0083XVCI.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-FF3-BinD-PCR4_S178_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4284VDSK/",
"accession": "IGVFFI4284VDSK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR3_S172"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:27:25.482500+00:00",
"file_format": "fastq",
"file_size": 18918595,
"href": "/sequence-files/IGVFFI4284VDSK/@@download/IGVFFI4284VDSK.fastq.gz",
"md5sum": "0a7b2bb266d0b4ef57d87894da4d755e",
"s3_uri": "s3://igvf-files/2024/06/03/de2c5dde-5859-434b-9c1f-8d25af4f9c60/IGVFFI4284VDSK.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-FF3-BinD-PCR3_S172_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": "2024-07-10T19:45:26.095467+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9423PKNV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9423PKNV",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR1_S76",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR2_S82",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR3_S172",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF3-BinD-PCR4_S178"
],
"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 D for 55-65% 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": "2024-06-03T15:26:53.207664+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": "a4e53a50-ca1d-47fe-9fba-01046aff3936"
}