{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1817YVNX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1817YVNX",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR1_S62",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR2_S68",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S158",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR4_S164"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"ERROR": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1817YVNX](/measurement-sets/IGVFDS1817YVNX/) links to sample [IGVFSM9298VRIP](/in-vitro-systems/IGVFSM9298VRIP/) which links to auxiliary set [IGVFDS8781ZUPM](/auxiliary-sets/IGVFDS8781ZUPM/) but is not in its `auxiliary_sets`. Measurement sets are expected to link to auxiliary sets if they share the same sample.",
"level": 60,
"level_name": "ERROR",
"name": "audit_missing_auxiliary_set_link",
"path": "/measurement-sets/IGVFDS1817YVNX/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1817YVNX](/measurement-sets/IGVFDS1817YVNX/) 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/IGVFDS1817YVNX/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1817YVNX](/measurement-sets/IGVFDS1817YVNX/) has sequence file(s) [IGVFFI2595DTOA](/sequence-files/IGVFFI2595DTOA/), [IGVFFI1326FOXQ](/sequence-files/IGVFFI1326FOXQ/), [IGVFFI2462KGZI](/sequence-files/IGVFFI2462KGZI/), [IGVFFI7411OJZE](/sequence-files/IGVFFI7411OJZE/) 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/IGVFDS1817YVNX/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1817YVNX](/measurement-sets/IGVFDS1817YVNX/) has revoked subobject auxiliary set [IGVFDS1008MWKE](/auxiliary-sets/IGVFDS1008MWKE/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1817YVNX/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9298VRIP](/in-vitro-systems/IGVFSM9298VRIP/) 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/IGVFSM9298VRIP/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Auxiliary set [IGVFDS1008MWKE](/auxiliary-sets/IGVFDS1008MWKE/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/auxiliary-sets/IGVFDS1008MWKE/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1817YVNX](/measurement-sets/IGVFDS1817YVNX/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS1817YVNX/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9298VRIP](/in-vitro-systems/IGVFSM9298VRIP/) 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/IGVFSM9298VRIP/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1008MWKE/",
"accession": "IGVFDS1008MWKE",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR1_S62",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR2_S68",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S158",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR4_S164"
],
"file_set_type": "gRNA sequencing",
"status": "revoked"
}
],
"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": "2024-05-16T17:56:53.634438+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/IGVFFI6970XEOM/",
"accession": "IGVFFI6970XEOM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR2_S68"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:35.677337+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI6970XEOM/@@download/IGVFFI6970XEOM.yaml.gz",
"md5sum": "df2ac2dfcbfd10232a02e4f61aded2df",
"s3_uri": "s3://igvf-files/2024/06/11/45d426a7-a568-456e-9695-f9d548085c6c/IGVFFI6970XEOM.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinB-PCR2_S68.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4650RNWL/",
"accession": "IGVFFI4650RNWL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR4_S164"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:07.437880+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI4650RNWL/@@download/IGVFFI4650RNWL.yaml.gz",
"md5sum": "5842e1f5b572f3f2ef67a7fcc05bdf44",
"s3_uri": "s3://igvf-files/2024/06/11/711d8dee-0376-4f32-9ffc-08deed6d2114/IGVFFI4650RNWL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinB-PCR4_S164.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI2595DTOA/",
"accession": "IGVFFI2595DTOA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S158"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:26:09.325596+00:00",
"file_format": "fastq",
"file_size": 25592663,
"href": "/sequence-files/IGVFFI2595DTOA/@@download/IGVFFI2595DTOA.fastq.gz",
"md5sum": "03cbf7534d3809d7f861d209b8c3f836",
"s3_uri": "s3://igvf-files/2024/06/03/428472d2-4963-4c4a-a1cd-d087b210806d/IGVFFI2595DTOA.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-FF2-BinB-PCR3_S158_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6604LVOF/",
"accession": "IGVFFI6604LVOF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR1_S62"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:20.701175+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI6604LVOF/@@download/IGVFFI6604LVOF.yaml.gz",
"md5sum": "91ac80abbba74496daf288db7b7754af",
"s3_uri": "s3://igvf-files/2024/06/11/7931a811-2f0b-46de-b283-35ee16597c35/IGVFFI6604LVOF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinB-PCR1_S62.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8100TPVI/",
"accession": "IGVFFI8100TPVI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S158"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:50.516145+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI8100TPVI/@@download/IGVFFI8100TPVI.yaml.gz",
"md5sum": "0b299c196be9aafded5b50809ca7ebf7",
"s3_uri": "s3://igvf-files/2024/06/11/85f3be8a-1036-4171-8a4b-a96d4f68ecf1/IGVFFI8100TPVI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinB-PCR3_S158.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1326FOXQ/",
"accession": "IGVFFI1326FOXQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR4_S164"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:26:30.302441+00:00",
"file_format": "fastq",
"file_size": 19755910,
"href": "/sequence-files/IGVFFI1326FOXQ/@@download/IGVFFI1326FOXQ.fastq.gz",
"md5sum": "a0a2eecb0d59333febcf9de064ff554a",
"s3_uri": "s3://igvf-files/2024/06/03/d9b12ef3-1c9f-43d9-a553-93e7a2fbc126/IGVFFI1326FOXQ.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-FF2-BinB-PCR4_S164_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2462KGZI/",
"accession": "IGVFFI2462KGZI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR1_S62"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:22:28.935540+00:00",
"file_format": "fastq",
"file_size": 15992476,
"href": "/sequence-files/IGVFFI2462KGZI/@@download/IGVFFI2462KGZI.fastq.gz",
"md5sum": "2ebaf9a2e9773ee44110fb1db734785c",
"s3_uri": "s3://igvf-files/2024/06/03/7e7d6514-bcae-4ab7-9805-5169c11ace97/IGVFFI2462KGZI.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-FF2-BinB-PCR1_S62_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7411OJZE/",
"accession": "IGVFFI7411OJZE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR2_S68"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:22:45.889065+00:00",
"file_format": "fastq",
"file_size": 12336642,
"href": "/sequence-files/IGVFFI7411OJZE/@@download/IGVFFI7411OJZE.fastq.gz",
"md5sum": "e13de992de4cb4c1d8590562eaa7b65a",
"s3_uri": "s3://igvf-files/2024/06/03/11774e2c-d219-4a65-895c-260c5d3b11b2/IGVFFI7411OJZE.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-FF2-BinB-PCR2_S68_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": "2024-07-10T19:44:41.947040+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9298VRIP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9298VRIP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR1_S62",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR2_S68",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR3_S158",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinB-PCR4_S164"
],
"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 B for 10-20% 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": "2024-06-03T15:22:28.935540+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": "84e216ff-cf96-497b-9878-eee8d4363c5b"
}