{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2046SNMC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2046SNMC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR1_S75",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR2_S171",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR3_S267",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR4_S363"
],
"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 [IGVFDS2046SNMC](/measurement-sets/IGVFDS2046SNMC/) 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/IGVFDS2046SNMC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2046SNMC](/measurement-sets/IGVFDS2046SNMC/) has sequence file(s) [IGVFFI1779JDBV](/sequence-files/IGVFFI1779JDBV/), [IGVFFI3891DAKN](/sequence-files/IGVFFI3891DAKN/), [IGVFFI3057BHFY](/sequence-files/IGVFFI3057BHFY/), [IGVFFI2478ZHXM](/sequence-files/IGVFFI2478ZHXM/) 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/IGVFDS2046SNMC/"
},
{
"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 [IGVFSM5079ZTJX](/in-vitro-systems/IGVFSM5079ZTJX/) 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/IGVFSM5079ZTJX/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM5079ZTJX](/in-vitro-systems/IGVFSM5079ZTJX/) 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/IGVFSM5079ZTJX/"
}
]
},
"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": "2024-05-06T22:19:33.118133+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/IGVFFI2438PQQQ/",
"accession": "IGVFFI2438PQQQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR3_S267"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:19.112107+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI2438PQQQ/@@download/IGVFFI2438PQQQ.yaml.gz",
"md5sum": "00a19e5177c329935bd1f750e0462bb3",
"s3_uri": "s3://igvf-files/2024/06/11/9375b6a2-9400-46e8-8f71-37917a155c61/IGVFFI2438PQQQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinC-PCR3_S267.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1779JDBV/",
"accession": "IGVFFI1779JDBV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR3_S267"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:49.664817+00:00",
"file_format": "fastq",
"file_size": 6228237,
"href": "/sequence-files/IGVFFI1779JDBV/@@download/IGVFFI1779JDBV.fastq.gz",
"md5sum": "abaa639db34bcb5e41c69b5fd1bf0df7",
"s3_uri": "s3://igvf-files/2024/06/01/1c5816f5-fbb8-49e1-90be-a90bd5780a41/IGVFFI1779JDBV.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-BinC-PCR3_S267_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2303ZRST/",
"accession": "IGVFFI2303ZRST",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR1_S75"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:52.731950+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI2303ZRST/@@download/IGVFFI2303ZRST.yaml.gz",
"md5sum": "227fd9b17c2a680146de8af63d148d08",
"s3_uri": "s3://igvf-files/2024/06/11/c20379ac-6308-4ca0-b524-67c0978f5883/IGVFFI2303ZRST.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinC-PCR1_S75.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4790WUCA/",
"accession": "IGVFFI4790WUCA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR2_S171"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:05.847995+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI4790WUCA/@@download/IGVFFI4790WUCA.yaml.gz",
"md5sum": "fd53169792fe51cc4256737d9d519f8c",
"s3_uri": "s3://igvf-files/2024/06/11/47cf084d-f5cf-4caa-b1b8-ec41a2d82ebf/IGVFFI4790WUCA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinC-PCR2_S171.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3891DAKN/",
"accession": "IGVFFI3891DAKN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR2_S171"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:33.319591+00:00",
"file_format": "fastq",
"file_size": 6894019,
"href": "/sequence-files/IGVFFI3891DAKN/@@download/IGVFFI3891DAKN.fastq.gz",
"md5sum": "773755b44f3222746505d326d691cbc6",
"s3_uri": "s3://igvf-files/2024/06/01/654217a7-abdd-4a1e-bbd7-07dd9ede9499/IGVFFI3891DAKN.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-BinC-PCR2_S171_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7524EEOV/",
"accession": "IGVFFI7524EEOV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR4_S363"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:32.368108+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI7524EEOV/@@download/IGVFFI7524EEOV.yaml.gz",
"md5sum": "f2bf0888f6896f4408bab4501ca99865",
"s3_uri": "s3://igvf-files/2024/06/11/c977f16f-498d-4d6b-b0af-a5acf2cf55cc/IGVFFI7524EEOV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinC-PCR4_S363.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3057BHFY/",
"accession": "IGVFFI3057BHFY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR4_S363"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:30:06.111033+00:00",
"file_format": "fastq",
"file_size": 6268071,
"href": "/sequence-files/IGVFFI3057BHFY/@@download/IGVFFI3057BHFY.fastq.gz",
"md5sum": "0663981d16d32760d6a5ed7e987ba7ed",
"s3_uri": "s3://igvf-files/2024/06/01/8606e457-c3b5-419b-9fec-73fd395b58c9/IGVFFI3057BHFY.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-BinC-PCR4_S363_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2478ZHXM/",
"accession": "IGVFFI2478ZHXM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR1_S75"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:17.578944+00:00",
"file_format": "fastq",
"file_size": 3094136,
"href": "/sequence-files/IGVFFI2478ZHXM/@@download/IGVFFI2478ZHXM.fastq.gz",
"md5sum": "1289ad9a528cc14b4bc1b367770651ae",
"s3_uri": "s3://igvf-files/2024/06/01/6d5d4317-a2b6-43fe-b3f9-93f5d839303a/IGVFFI2478ZHXM.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-BinC-PCR1_S75_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": "2024-07-10T19:49:27.331307+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5079ZTJX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5079ZTJX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR1_S75",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR2_S171",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR3_S267",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinC-PCR4_S363"
],
"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 C for 35-45% 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": "2024-06-01T01:29:17.578944+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": "ad3c51b1-37d9-464a-9391-bb0e164e42ac"
}