{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8517JVOP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8517JVOP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR1_S3",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR2_S9",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR3_S99",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR4_S105"
],
"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 [IGVFSM2684MUBP](/in-vitro-systems/IGVFSM2684MUBP/) 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/IGVFSM2684MUBP/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8517JVOP](/measurement-sets/IGVFDS8517JVOP/) 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/IGVFDS8517JVOP/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8517JVOP](/measurement-sets/IGVFDS8517JVOP/) has sequence file(s) [IGVFFI9296GYRI](/sequence-files/IGVFFI9296GYRI/), [IGVFFI5868RORR](/sequence-files/IGVFFI5868RORR/), [IGVFFI5595DRFH](/sequence-files/IGVFFI5595DRFH/), [IGVFFI3826HBLM](/sequence-files/IGVFFI3826HBLM/) 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/IGVFDS8517JVOP/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS9621FJCZ](/auxiliary-sets/IGVFDS9621FJCZ/) 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/IGVFDS9621FJCZ/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2684MUBP](/in-vitro-systems/IGVFSM2684MUBP/) 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/IGVFSM2684MUBP/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9621FJCZ/",
"accession": "IGVFDS9621FJCZ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin0hrs-FF1"
],
"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": "2024-05-16T17:32:29.702060+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/IGVFFI0591NEKK/",
"accession": "IGVFFI0591NEKK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR1_S3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:45.503390+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI0591NEKK/@@download/IGVFFI0591NEKK.yaml.gz",
"md5sum": "4500fa8ee0d87f479d628e7bab461d57",
"s3_uri": "s3://igvf-files/2024/06/11/9f974a3e-f12a-4785-a1cd-f57f3a37c79f/IGVFFI0591NEKK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinC-PCR1_S3.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9956ZGCK/",
"accession": "IGVFFI9956ZGCK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR2_S9"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:59.080270+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI9956ZGCK/@@download/IGVFFI9956ZGCK.yaml.gz",
"md5sum": "50eb969ce1c5e01f6aef51886664aa75",
"s3_uri": "s3://igvf-files/2024/06/11/2ac716d1-da2a-48c7-bcbd-332c4212512d/IGVFFI9956ZGCK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinC-PCR2_S9.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0733SJHF/",
"accession": "IGVFFI0733SJHF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR4_S105"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:26.022103+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI0733SJHF/@@download/IGVFFI0733SJHF.yaml.gz",
"md5sum": "cc3435155785ef7323199e447c7d1192",
"s3_uri": "s3://igvf-files/2024/06/11/457f58ff-b065-4596-b415-19b4b42d2a84/IGVFFI0733SJHF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinC-PCR4_S105.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9296GYRI/",
"accession": "IGVFFI9296GYRI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR3_S99"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:58.241094+00:00",
"file_format": "fastq",
"file_size": 36459691,
"href": "/sequence-files/IGVFFI9296GYRI/@@download/IGVFFI9296GYRI.fastq.gz",
"md5sum": "8ac50b3a2e596c5078d49b32002dd3d7",
"s3_uri": "s3://igvf-files/2024/06/01/8b69979d-78c0-4aee-bf58-44c998f12e6f/IGVFFI9296GYRI.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-FF1-BinC-PCR3_S99_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7508DSUR/",
"accession": "IGVFFI7508DSUR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR3_S99"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:12.707719+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI7508DSUR/@@download/IGVFFI7508DSUR.yaml.gz",
"md5sum": "3a0d3a799b68eca8ed7055d2f9ec9fb8",
"s3_uri": "s3://igvf-files/2024/06/11/a6e03404-5427-4c7b-b3e7-f4f4dba1968e/IGVFFI7508DSUR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinC-PCR3_S99.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5868RORR/",
"accession": "IGVFFI5868RORR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR1_S3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:17.665589+00:00",
"file_format": "fastq",
"file_size": 17580393,
"href": "/sequence-files/IGVFFI5868RORR/@@download/IGVFFI5868RORR.fastq.gz",
"md5sum": "6832b3b306945d9d719903f07bea3ada",
"s3_uri": "s3://igvf-files/2024/06/01/d2a27622-0d80-473a-b064-05d02f0ee963/IGVFFI5868RORR.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-FF1-BinC-PCR1_S3_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5595DRFH/",
"accession": "IGVFFI5595DRFH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR2_S9"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:40.157687+00:00",
"file_format": "fastq",
"file_size": 13628899,
"href": "/sequence-files/IGVFFI5595DRFH/@@download/IGVFFI5595DRFH.fastq.gz",
"md5sum": "755ec64164f72ade59e6a3c4be6dd7b5",
"s3_uri": "s3://igvf-files/2024/06/01/cfc2dab3-90ea-4e73-a2f7-1508d7474868/IGVFFI5595DRFH.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-FF1-BinC-PCR2_S9_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3826HBLM/",
"accession": "IGVFFI3826HBLM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR4_S105"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:11:16.363458+00:00",
"file_format": "fastq",
"file_size": 33815951,
"href": "/sequence-files/IGVFFI3826HBLM/@@download/IGVFFI3826HBLM.fastq.gz",
"md5sum": "13a6371e5d192a0127caba0cfd2e3ffc",
"s3_uri": "s3://igvf-files/2024/06/01/e9fe4f0a-2ed9-4949-919b-c47faab90dd2/IGVFFI3826HBLM.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-FF1-BinC-PCR4_S105_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": "2024-07-10T19:42:04.954187+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2684MUBP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2684MUBP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR1_S3",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR2_S9",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR3_S99",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinC-PCR4_S105"
],
"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 C for 35-45% 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": "2024-06-01T02:10:17.665589+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": "332bf3fc-66e6-45bc-bb68-2d36d52a40cf"
}