{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1679JOIX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1679JOIX",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
],
"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 [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/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1679JOIX](/measurement-sets/IGVFDS1679JOIX/) 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/IGVFDS1679JOIX/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1679JOIX](/measurement-sets/IGVFDS1679JOIX/) has sequence file(s) [IGVFFI2660UTOF](/sequence-files/IGVFFI2660UTOF/), [IGVFFI0357RECW](/sequence-files/IGVFFI0357RECW/), [IGVFFI0079YAMM](/sequence-files/IGVFFI0079YAMM/), [IGVFFI7682PLQL](/sequence-files/IGVFFI7682PLQL/) 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/IGVFDS1679JOIX/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4469TBGW](/in-vitro-systems/IGVFSM4469TBGW/) 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/IGVFSM4469TBGW/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM4469TBGW](/in-vitro-systems/IGVFSM4469TBGW/) 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/IGVFSM4469TBGW/"
}
]
},
"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": "2024-05-16T17:32:27.934189+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/IGVFFI6958FQNG/",
"accession": "IGVFFI6958FQNG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:42.644512+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI6958FQNG/@@download/IGVFFI6958FQNG.yaml.gz",
"md5sum": "867b2f7c7c96b918a8eb473440eb4294",
"s3_uri": "s3://igvf-files/2024/06/11/9ffcc9c7-bcb3-429a-96b5-1c0b91fc3d22/IGVFFI6958FQNG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR1_S2.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6721VKWR/",
"accession": "IGVFFI6721VKWR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:10.471658+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI6721VKWR/@@download/IGVFFI6721VKWR.yaml.gz",
"md5sum": "f542c51b446722b0be1c34dd5bd6283c",
"s3_uri": "s3://igvf-files/2024/06/11/712800c8-4045-4c16-949c-b8ae61f947cf/IGVFFI6721VKWR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR3_S98.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3962TRBT/",
"accession": "IGVFFI3962TRBT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:56.882382+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI3962TRBT/@@download/IGVFFI3962TRBT.yaml.gz",
"md5sum": "af6ca2be0f7218436e333f87223d71aa",
"s3_uri": "s3://igvf-files/2024/06/11/4b2aa2a9-fc18-40cf-8d5d-5abf28eccf8f/IGVFFI3962TRBT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR2_S8.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8059ZOIT/",
"accession": "IGVFFI8059ZOIT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:23.697671+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI8059ZOIT/@@download/IGVFFI8059ZOIT.yaml.gz",
"md5sum": "c3df018ebbfaeb96fa0bac37f49472f2",
"s3_uri": "s3://igvf-files/2024/06/11/e99a5bd6-3a30-4e37-b249-9134d0cedd17/IGVFFI8059ZOIT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR4_S104.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI2660UTOF/",
"accession": "IGVFFI2660UTOF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:33.277352+00:00",
"file_format": "fastq",
"file_size": 12033624,
"href": "/sequence-files/IGVFFI2660UTOF/@@download/IGVFFI2660UTOF.fastq.gz",
"md5sum": "b3923191ed77eb09b1a7f79c3ab82625",
"s3_uri": "s3://igvf-files/2024/06/01/9e67465c-0499-4e06-8669-943c21a7644b/IGVFFI2660UTOF.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-BinB-PCR2_S8_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0357RECW/",
"accession": "IGVFFI0357RECW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:14.444737+00:00",
"file_format": "fastq",
"file_size": 17777080,
"href": "/sequence-files/IGVFFI0357RECW/@@download/IGVFFI0357RECW.fastq.gz",
"md5sum": "9a763327d8b46b1306e77e65b8381436",
"s3_uri": "s3://igvf-files/2024/06/01/d6ba4e2b-9d9d-46d5-abd2-fbf5ae98274c/IGVFFI0357RECW.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-BinB-PCR1_S2_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0079YAMM/",
"accession": "IGVFFI0079YAMM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:55.160854+00:00",
"file_format": "fastq",
"file_size": 40391210,
"href": "/sequence-files/IGVFFI0079YAMM/@@download/IGVFFI0079YAMM.fastq.gz",
"md5sum": "17439f2d67cb9e29c43818a29a3aed1c",
"s3_uri": "s3://igvf-files/2024/06/01/c37dea70-4c22-471e-8ef0-97af0e2f5a4e/IGVFFI0079YAMM.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-BinB-PCR3_S98_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7682PLQL/",
"accession": "IGVFFI7682PLQL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:11:13.396167+00:00",
"file_format": "fastq",
"file_size": 23961767,
"href": "/sequence-files/IGVFFI7682PLQL/@@download/IGVFFI7682PLQL.fastq.gz",
"md5sum": "a8a3c042a2d9767611eb407ab0d35985",
"s3_uri": "s3://igvf-files/2024/06/01/331fdc20-281c-4047-9495-aae48f0a4a43/IGVFFI7682PLQL.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-BinB-PCR4_S104_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": "2024-07-10T19:41:58.356156+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4469TBGW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4469TBGW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
],
"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": "2024-06-01T02:10:14.444737+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": "49214dcf-0956-4b02-8117-7c936deea4a0"
}