{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0548YILY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0548YILY",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR1_S65",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR2_S71",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR3_S161",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR4_S167"
],
"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 [IGVFSM4441KRKU](/in-vitro-systems/IGVFSM4441KRKU/) 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/IGVFSM4441KRKU/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0548YILY](/measurement-sets/IGVFDS0548YILY/) 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/IGVFDS0548YILY/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0548YILY](/measurement-sets/IGVFDS0548YILY/) has sequence file(s) [IGVFFI8901VLCQ](/sequence-files/IGVFFI8901VLCQ/), [IGVFFI3706KVDE](/sequence-files/IGVFFI3706KVDE/), [IGVFFI9347INON](/sequence-files/IGVFFI9347INON/), [IGVFFI2496VSIB](/sequence-files/IGVFFI2496VSIB/) 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/IGVFDS0548YILY/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS8781ZUPM](/auxiliary-sets/IGVFDS8781ZUPM/) 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/IGVFDS8781ZUPM/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM4441KRKU](/in-vitro-systems/IGVFSM4441KRKU/) 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/IGVFSM4441KRKU/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8781ZUPM/",
"accession": "IGVFDS8781ZUPM",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin6hrs-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": "2024-05-16T17:56:57.526057+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/IGVFFI5245IYGK/",
"accession": "IGVFFI5245IYGK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR3_S161"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:00.223354+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI5245IYGK/@@download/IGVFFI5245IYGK.yaml.gz",
"md5sum": "5c4989c9d94f53d8643c4864b1076856",
"s3_uri": "s3://igvf-files/2024/06/11/36cb5b09-3cce-4e89-ac68-d0cd461f709e/IGVFFI5245IYGK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinE-PCR3_S161.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI5203MRMY/",
"accession": "IGVFFI5203MRMY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR2_S71"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:43.115072+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI5203MRMY/@@download/IGVFFI5203MRMY.yaml.gz",
"md5sum": "1a1d752244dfbe1f52b94ba6190a004a",
"s3_uri": "s3://igvf-files/2024/06/11/e0d2194e-d035-4c81-a89a-c119fa45c7e2/IGVFFI5203MRMY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinE-PCR2_S71.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8901VLCQ/",
"accession": "IGVFFI8901VLCQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR3_S161"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:26:18.022484+00:00",
"file_format": "fastq",
"file_size": 27447252,
"href": "/sequence-files/IGVFFI8901VLCQ/@@download/IGVFFI8901VLCQ.fastq.gz",
"md5sum": "cfc48a09b5f65d8968dfa8f713fa286e",
"s3_uri": "s3://igvf-files/2024/06/03/4b1c95f0-bb2d-4ca6-94e9-e5844aae3852/IGVFFI8901VLCQ.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-BinE-PCR3_S161_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3706KVDE/",
"accession": "IGVFFI3706KVDE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR2_S71"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:22:54.065163+00:00",
"file_format": "fastq",
"file_size": 10247671,
"href": "/sequence-files/IGVFFI3706KVDE/@@download/IGVFFI3706KVDE.fastq.gz",
"md5sum": "97ee4cb0eed7a6f9b36afc75fee4c9e4",
"s3_uri": "s3://igvf-files/2024/06/03/e3e0b014-7c32-4012-8d33-3c7575cf2f29/IGVFFI3706KVDE.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-BinE-PCR2_S71_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8401BOPY/",
"accession": "IGVFFI8401BOPY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR4_S167"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:11:14.548748+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI8401BOPY/@@download/IGVFFI8401BOPY.yaml.gz",
"md5sum": "f06f00f7b19f909e69c5254a1beef1f2",
"s3_uri": "s3://igvf-files/2024/06/11/540bec21-b98c-4c19-aee1-93642f126c10/IGVFFI8401BOPY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinE-PCR4_S167.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0348GTHV/",
"accession": "IGVFFI0348GTHV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR1_S65"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:28.364332+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI0348GTHV/@@download/IGVFFI0348GTHV.yaml.gz",
"md5sum": "7b18e7632b4223ccfb1ccb829a23f3de",
"s3_uri": "s3://igvf-files/2024/06/11/11febd52-8c0b-49f9-8dce-bbb028e9a1f1/IGVFFI0348GTHV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF2-BinE-PCR1_S65.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9347INON/",
"accession": "IGVFFI9347INON",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR4_S167"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:26:39.094421+00:00",
"file_format": "fastq",
"file_size": 18989850,
"href": "/sequence-files/IGVFFI9347INON/@@download/IGVFFI9347INON.fastq.gz",
"md5sum": "801a2e6b795f73cafb19aa68ddcbb311",
"s3_uri": "s3://igvf-files/2024/06/03/e89cfb2b-3c49-4fc3-9401-a8eae098ce14/IGVFFI9347INON.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-BinE-PCR4_S167_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2496VSIB/",
"accession": "IGVFFI2496VSIB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR1_S65"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:22:37.706324+00:00",
"file_format": "fastq",
"file_size": 11268605,
"href": "/sequence-files/IGVFFI2496VSIB/@@download/IGVFFI2496VSIB.fastq.gz",
"md5sum": "28bea971b4db6e2331979fa3e4aac53e",
"s3_uri": "s3://igvf-files/2024/06/03/317fe048-ccf9-445c-a7c6-37f8d0dea87d/IGVFFI2496VSIB.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-BinE-PCR1_S65_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": "2024-07-10T19:44:57.023248+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4441KRKU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4441KRKU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR1_S65",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR2_S71",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR3_S161",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF2-BinE-PCR4_S167"
],
"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 E for 80-90% 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": "2024-06-03T15:22:37.706324+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": "15cb70ea-3d94-4190-a93c-f0eb3deae611"
}