{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7147ANAC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7147ANAC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR1_S14",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116"
],
"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 [IGVFDS4522DABT](/auxiliary-sets/IGVFDS4522DABT/) 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/IGVFDS4522DABT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3263KXLP](/in-vitro-systems/IGVFSM3263KXLP/) 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/IGVFSM3263KXLP/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7147ANAC](/measurement-sets/IGVFDS7147ANAC/) 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/IGVFDS7147ANAC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7147ANAC](/measurement-sets/IGVFDS7147ANAC/) has sequence file(s) [IGVFFI3742XLEW](/sequence-files/IGVFFI3742XLEW/), [IGVFFI2295FIDE](/sequence-files/IGVFFI2295FIDE/), [IGVFFI6322UNED](/sequence-files/IGVFFI6322UNED/), [IGVFFI1480XPQY](/sequence-files/IGVFFI1480XPQY/) 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/IGVFDS7147ANAC/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3263KXLP](/in-vitro-systems/IGVFSM3263KXLP/) 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/IGVFSM3263KXLP/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4522DABT/",
"accession": "IGVFDS4522DABT",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin0hrs-FF2"
],
"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": "2024-05-16T17:32:57.155098+00:00",
"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/IGVFFI0936XUFD/",
"accession": "IGVFFI0936XUFD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:50.750952+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI0936XUFD/@@download/IGVFFI0936XUFD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9f7b92a2-ed0d-4605-9d61-041756886ea1/IGVFFI0936XUFD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinB-PCR2_S20.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0141MIOQ/",
"accession": "IGVFFI0141MIOQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:04.569484+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0141MIOQ/@@download/IGVFFI0141MIOQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cd1bf0b3-5adc-4641-92d0-f436efbd28f3/IGVFFI0141MIOQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinB-PCR3_S110.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3742XLEW/",
"accession": "IGVFFI3742XLEW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:50.249863+00:00",
"file_format": "fastq",
"file_size": 10426667,
"href": "/sequence-files/IGVFFI3742XLEW/@@download/IGVFFI3742XLEW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e48f4af8-1217-4d52-bd48-915fd4433eb9/IGVFFI3742XLEW.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-FF2-BinB-PCR2_S20_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1101JVSO/",
"accession": "IGVFFI1101JVSO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR1_S14"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:37.434450+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI1101JVSO/@@download/IGVFFI1101JVSO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f5241286-e55c-4fd4-8790-dce86654e02c/IGVFFI1101JVSO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinB-PCR1_S14.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8160QJHC/",
"accession": "IGVFFI8160QJHC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:17.713725+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI8160QJHC/@@download/IGVFFI8160QJHC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e2efbf39-2690-420a-b234-62621076d690/IGVFFI8160QJHC.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinB-PCR4_S116.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI2295FIDE/",
"accession": "IGVFFI2295FIDE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:16:51.905012+00:00",
"file_format": "fastq",
"file_size": 26958877,
"href": "/sequence-files/IGVFFI2295FIDE/@@download/IGVFFI2295FIDE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ed044620-4602-4b9b-8ac6-ccdbe609cf2b/IGVFFI2295FIDE.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-FF2-BinB-PCR3_S110_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6322UNED/",
"accession": "IGVFFI6322UNED",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR1_S14"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:32.672890+00:00",
"file_format": "fastq",
"file_size": 12935220,
"href": "/sequence-files/IGVFFI6322UNED/@@download/IGVFFI6322UNED.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/73b62078-85ac-448b-a8ff-282b1517d103/IGVFFI6322UNED.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-FF2-BinB-PCR1_S14_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1480XPQY/",
"accession": "IGVFFI1480XPQY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:17:10.409332+00:00",
"file_format": "fastq",
"file_size": 21673848,
"href": "/sequence-files/IGVFFI1480XPQY/@@download/IGVFFI1480XPQY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/13434af9-a1a5-46eb-a7e5-17429408565a/IGVFFI1480XPQY.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-FF2-BinB-PCR4_S116_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": "2024-07-10T19:42:32.841306+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3263KXLP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3263KXLP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR1_S14",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116"
],
"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": "2024-06-01T02:14:32.672890+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": "fc9ab042-6677-4c24-9a08-261355a7f363"
}