{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6007VHUG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6007VHUG",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
],
"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 [IGVFSM3068ZYXS](/in-vitro-systems/IGVFSM3068ZYXS/) 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/IGVFSM3068ZYXS/"
},
{
"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": "Measurement set [IGVFDS6007VHUG](/measurement-sets/IGVFDS6007VHUG/) 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/IGVFDS6007VHUG/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6007VHUG](/measurement-sets/IGVFDS6007VHUG/) has sequence file(s) [IGVFFI1457EKWS](/sequence-files/IGVFFI1457EKWS/), [IGVFFI4376KAKY](/sequence-files/IGVFFI4376KAKY/), [IGVFFI4369YDEU](/sequence-files/IGVFFI4369YDEU/), [IGVFFI6514JTIC](/sequence-files/IGVFFI6514JTIC/) 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/IGVFDS6007VHUG/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3068ZYXS](/in-vitro-systems/IGVFSM3068ZYXS/) 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/IGVFSM3068ZYXS/"
}
]
},
"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": "2024-05-16T17:33:22.109179+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/IGVFFI5189ZWRI/",
"accession": "IGVFFI5189ZWRI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:15.623998+00:00",
"file_format": "yaml",
"file_size": 905,
"href": "/configuration-files/IGVFFI5189ZWRI/@@download/IGVFFI5189ZWRI.yaml.gz",
"md5sum": "7034073d4ab2efc55740c58698249c04",
"s3_uri": "s3://igvf-files/2024/06/11/b8c5f31f-2cde-4c8e-8afe-0b59ca558b9b/IGVFFI5189ZWRI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR4_S130.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1457EKWS/",
"accession": "IGVFFI1457EKWS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:33.774408+00:00",
"file_format": "fastq",
"file_size": 9690717,
"href": "/sequence-files/IGVFFI1457EKWS/@@download/IGVFFI1457EKWS.fastq.gz",
"md5sum": "81003c5a27931373d352519556ba0d29",
"s3_uri": "s3://igvf-files/2024/06/01/0e9b4aa7-de8e-495d-b4ac-7457d0263f91/IGVFFI1457EKWS.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-BinD-PCR1_S28_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1137LHCT/",
"accession": "IGVFFI1137LHCT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:02.351965+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI1137LHCT/@@download/IGVFFI1137LHCT.yaml.gz",
"md5sum": "9908f8676314e21652da11a9ec3cd7e3",
"s3_uri": "s3://igvf-files/2024/06/11/0aae9ad4-6a8b-4540-a350-d8d1ab9f87bd/IGVFFI1137LHCT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR3_S124.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1149KOYD/",
"accession": "IGVFFI1149KOYD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:35.760798+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1149KOYD/@@download/IGVFFI1149KOYD.yaml.gz",
"md5sum": "9937261979d0895619e7616167ef9ea0",
"s3_uri": "s3://igvf-files/2024/06/11/5efd1b99-5540-4a78-9c05-4fd02b7ae686/IGVFFI1149KOYD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR1_S28.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4376KAKY/",
"accession": "IGVFFI4376KAKY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:51.855556+00:00",
"file_format": "fastq",
"file_size": 10933667,
"href": "/sequence-files/IGVFFI4376KAKY/@@download/IGVFFI4376KAKY.fastq.gz",
"md5sum": "a4bd93ff6cc57b9b0e29057db71b6da8",
"s3_uri": "s3://igvf-files/2024/06/01/09edb302-5744-4d76-99bc-fc8459a75105/IGVFFI4376KAKY.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-BinD-PCR2_S34_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4369YDEU/",
"accession": "IGVFFI4369YDEU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:27.785290+00:00",
"file_format": "fastq",
"file_size": 20531648,
"href": "/sequence-files/IGVFFI4369YDEU/@@download/IGVFFI4369YDEU.fastq.gz",
"md5sum": "b3b7704046e8de48bdf065d6108b4e0f",
"s3_uri": "s3://igvf-files/2024/06/01/1a7b76b3-afd6-40ed-aa66-fce0d3509606/IGVFFI4369YDEU.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-BinD-PCR4_S130_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7135SUWD/",
"accession": "IGVFFI7135SUWD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:49.107063+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI7135SUWD/@@download/IGVFFI7135SUWD.yaml.gz",
"md5sum": "6bd66500a8e403afac1908de2dc616f5",
"s3_uri": "s3://igvf-files/2024/06/11/7b91610b-f973-4802-8c66-6dcf41ff21ac/IGVFFI7135SUWD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR2_S34.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI6514JTIC/",
"accession": "IGVFFI6514JTIC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:18:09.739332+00:00",
"file_format": "fastq",
"file_size": 14976861,
"href": "/sequence-files/IGVFFI6514JTIC/@@download/IGVFFI6514JTIC.fastq.gz",
"md5sum": "2ab130f984cc04c552972f29cbd39edc",
"s3_uri": "s3://igvf-files/2024/06/01/1e3ad7b9-fb63-41a1-a4cd-cdd3cac19a9a/IGVFFI6514JTIC.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-BinD-PCR3_S124_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": "2024-07-10T19:43:17.671427+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3068ZYXS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3068ZYXS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
],
"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 D for 55-65% 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": "2024-06-01T02:17:33.774408+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": "77a70c49-a9d6-4819-8fbd-dcf476ec889d"
}