{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1099HASC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1099HASC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR1_S74",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR2_S170",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR3_S266",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR4_S362"
],
"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": "Measurement set [IGVFDS1099HASC](/measurement-sets/IGVFDS1099HASC/) 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/IGVFDS1099HASC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1099HASC](/measurement-sets/IGVFDS1099HASC/) has sequence file(s) [IGVFFI8028SAKO](/sequence-files/IGVFFI8028SAKO/), [IGVFFI8999KUTF](/sequence-files/IGVFFI8999KUTF/), [IGVFFI8975NPWA](/sequence-files/IGVFFI8975NPWA/), [IGVFFI3757DBEL](/sequence-files/IGVFFI3757DBEL/) 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/IGVFDS1099HASC/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS5292OCBC](/auxiliary-sets/IGVFDS5292OCBC/) 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/IGVFDS5292OCBC/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7863HHJP](/in-vitro-systems/IGVFSM7863HHJP/) 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/IGVFSM7863HHJP/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7863HHJP](/in-vitro-systems/IGVFSM7863HHJP/) 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/IGVFSM7863HHJP/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5292OCBC/",
"accession": "IGVFDS5292OCBC",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_PILOT_CCND1-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/IGVFDS0392OWNZ/",
"accession": "IGVFDS0392OWNZ",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI4981YFMT/",
"accession": "IGVFFI4981YFMT",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in 36 genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-05-06T22:19:32.206636+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": "/sequence-files/IGVFFI8028SAKO/",
"accession": "IGVFFI8028SAKO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR4_S362"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:30:03.409589+00:00",
"file_format": "fastq",
"file_size": 7747947,
"href": "/sequence-files/IGVFFI8028SAKO/@@download/IGVFFI8028SAKO.fastq.gz",
"md5sum": "21f16df5ae8cdd18f7f87c7140f78a27",
"s3_uri": "s3://igvf-files/2024/06/01/e2db7edd-836e-4429-9fc8-f9527fde0854/IGVFFI8028SAKO.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/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinB-PCR4_S362_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1109UFAS/",
"accession": "IGVFFI1109UFAS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR2_S170"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:03.717066+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI1109UFAS/@@download/IGVFFI1109UFAS.yaml.gz",
"md5sum": "79018f72fa379450d8bb84068c858f02",
"s3_uri": "s3://igvf-files/2024/06/11/8b4c0e0b-03b1-4481-bdd8-7dd39d8af9dd/IGVFFI1109UFAS.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinB-PCR2_S170.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4385CMLD/",
"accession": "IGVFFI4385CMLD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR3_S266"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:16.902734+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI4385CMLD/@@download/IGVFFI4385CMLD.yaml.gz",
"md5sum": "630e0d2fae1476db4499b6778bbeb38a",
"s3_uri": "s3://igvf-files/2024/06/11/a389382f-e7bf-4eb5-b838-ffefab882d03/IGVFFI4385CMLD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinB-PCR3_S266.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9599NWTY/",
"accession": "IGVFFI9599NWTY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR1_S74"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:50.622609+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI9599NWTY/@@download/IGVFFI9599NWTY.yaml.gz",
"md5sum": "048dc0e1721292214b3c68290a224087",
"s3_uri": "s3://igvf-files/2024/06/11/d5673a47-c4cd-4390-906b-08bbf7fd45f9/IGVFFI9599NWTY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinB-PCR1_S74.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8999KUTF/",
"accession": "IGVFFI8999KUTF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR1_S74"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:14.939330+00:00",
"file_format": "fastq",
"file_size": 4916050,
"href": "/sequence-files/IGVFFI8999KUTF/@@download/IGVFFI8999KUTF.fastq.gz",
"md5sum": "1b86366a6d8bc06f0b91314d5248654f",
"s3_uri": "s3://igvf-files/2024/06/01/251e2f72-545e-4592-8496-305b669922a2/IGVFFI8999KUTF.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/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinB-PCR1_S74_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6277THMR/",
"accession": "IGVFFI6277THMR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR4_S362"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:30.215947+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI6277THMR/@@download/IGVFFI6277THMR.yaml.gz",
"md5sum": "493f3254105be12ebed25d1582aeada8",
"s3_uri": "s3://igvf-files/2024/06/11/f1a7f194-0ba8-4551-98fb-cde2c1993357/IGVFFI6277THMR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinB-PCR4_S362.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8975NPWA/",
"accession": "IGVFFI8975NPWA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR3_S266"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:46.762185+00:00",
"file_format": "fastq",
"file_size": 8541992,
"href": "/sequence-files/IGVFFI8975NPWA/@@download/IGVFFI8975NPWA.fastq.gz",
"md5sum": "ceeca611f7d54a0e994231a3e137508a",
"s3_uri": "s3://igvf-files/2024/06/01/9079b9fd-31e5-4a6d-af0a-25b06f9e19f7/IGVFFI8975NPWA.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/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinB-PCR3_S266_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3757DBEL/",
"accession": "IGVFFI3757DBEL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR2_S170"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:30.716573+00:00",
"file_format": "fastq",
"file_size": 6560633,
"href": "/sequence-files/IGVFFI3757DBEL/@@download/IGVFFI3757DBEL.fastq.gz",
"md5sum": "e19946ff8fa63f12994746901ab4d028",
"s3_uri": "s3://igvf-files/2024/06/01/042d017d-ab42-4d7f-897f-7a5d30a4a9ec/IGVFFI3757DBEL.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/210301B002-CohesinFF/fastq/CCND1-Auxin0hrs-FF1-BinB-PCR2_S170_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2982SJGW/"
],
"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": "2024-07-10T19:49:20.170550+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7863HHJP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7863HHJP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR1_S74",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR2_S170",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR3_S266",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinB-PCR4_S362"
],
"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 CCND1) 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": "2024-06-01T01:29:14.939330+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of CCND1 integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000110092/",
"geneid": "ENSG00000110092",
"name": "cyclin D1",
"status": "released",
"symbol": "CCND1",
"synonyms": [
"U21B31",
"cyclin D1",
"B-cell CLL/lymphoma 1",
"PRAD1 oncogene",
"PRAD1",
"CCND1",
"G1/S-specific cyclin-D1",
"BCL-1 oncogene",
"BCL1",
"D11S287E",
"B-cell lymphoma 1 protein"
]
}
],
"uuid": "2d0ef199-1688-49ae-adfd-76589daf8cab"
}