{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4315AMOI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4315AMOI",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR1_S78",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR2_S174",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR3_S270",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR4_S366"
],
"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 [IGVFDS4315AMOI](/measurement-sets/IGVFDS4315AMOI/) 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/IGVFDS4315AMOI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4315AMOI](/measurement-sets/IGVFDS4315AMOI/) has sequence file(s) [IGVFFI3801VJQA](/sequence-files/IGVFFI3801VJQA/), [IGVFFI6403RRAQ](/sequence-files/IGVFFI6403RRAQ/), [IGVFFI6162BDDF](/sequence-files/IGVFFI6162BDDF/), [IGVFFI0939JLGV](/sequence-files/IGVFFI0939JLGV/) 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/IGVFDS4315AMOI/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4674ZTIR](/in-vitro-systems/IGVFSM4674ZTIR/) 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/IGVFSM4674ZTIR/"
},
{
"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/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM4674ZTIR](/in-vitro-systems/IGVFSM4674ZTIR/) 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/IGVFSM4674ZTIR/"
}
]
},
"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": "2024-05-06T22:29:11.047541+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/IGVFFI6703EYJY/",
"accession": "IGVFFI6703EYJY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR3_S270"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:25.818290+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI6703EYJY/@@download/IGVFFI6703EYJY.yaml.gz",
"md5sum": "9b85307bcc26fd05410207f8eefb3501",
"s3_uri": "s3://igvf-files/2024/06/11/cb716eee-1d3b-4ad5-858e-e60b8a3b747e/IGVFFI6703EYJY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinF-PCR3_S270.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI5866GGCP/",
"accession": "IGVFFI5866GGCP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR1_S78"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:59.303294+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI5866GGCP/@@download/IGVFFI5866GGCP.yaml.gz",
"md5sum": "bbfdae65d2679e343436cf6f587415da",
"s3_uri": "s3://igvf-files/2024/06/11/070e3d7f-24c6-4f74-8b3d-455769a5d14a/IGVFFI5866GGCP.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinF-PCR1_S78.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4141UFVD/",
"accession": "IGVFFI4141UFVD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR2_S174"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:12.523815+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI4141UFVD/@@download/IGVFFI4141UFVD.yaml.gz",
"md5sum": "25865b0d3273b4835d5c103638898625",
"s3_uri": "s3://igvf-files/2024/06/11/facdbd7d-9caf-4e45-9fee-a31ed36a00fd/IGVFFI4141UFVD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinF-PCR2_S174.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3801VJQA/",
"accession": "IGVFFI3801VJQA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR3_S270"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:58.181584+00:00",
"file_format": "fastq",
"file_size": 4111862,
"href": "/sequence-files/IGVFFI3801VJQA/@@download/IGVFFI3801VJQA.fastq.gz",
"md5sum": "49f66f8290781d230de20678091bcaeb",
"s3_uri": "s3://igvf-files/2024/06/01/e87f2da8-afda-4b4f-9693-62b7dc5dcc0e/IGVFFI3801VJQA.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-BinF-PCR3_S270_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8008FYNH/",
"accession": "IGVFFI8008FYNH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR4_S366"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:24:39.130810+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI8008FYNH/@@download/IGVFFI8008FYNH.yaml.gz",
"md5sum": "f430fcfb8e1f02baf8f5dcbc2e7ff632",
"s3_uri": "s3://igvf-files/2024/06/11/ad3030d3-262f-4044-8190-26ed4ca11aaf/IGVFFI8008FYNH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin0hrs-FF1-BinF-PCR4_S366.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI6403RRAQ/",
"accession": "IGVFFI6403RRAQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR4_S366"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:30:14.502707+00:00",
"file_format": "fastq",
"file_size": 3642809,
"href": "/sequence-files/IGVFFI6403RRAQ/@@download/IGVFFI6403RRAQ.fastq.gz",
"md5sum": "31f517a121c5bc55a267bd115d5ddbe1",
"s3_uri": "s3://igvf-files/2024/06/01/b9d74197-67f4-4325-b209-2be1ab145517/IGVFFI6403RRAQ.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-BinF-PCR4_S366_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6162BDDF/",
"accession": "IGVFFI6162BDDF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR1_S78"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:25.532695+00:00",
"file_format": "fastq",
"file_size": 2823910,
"href": "/sequence-files/IGVFFI6162BDDF/@@download/IGVFFI6162BDDF.fastq.gz",
"md5sum": "fae99f23af63b2a4396dce195c39d74a",
"s3_uri": "s3://igvf-files/2024/06/01/78c75c05-a774-45ee-a508-3cef2d39580e/IGVFFI6162BDDF.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-BinF-PCR1_S78_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0939JLGV/",
"accession": "IGVFFI0939JLGV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR2_S174"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:29:41.334054+00:00",
"file_format": "fastq",
"file_size": 2754590,
"href": "/sequence-files/IGVFFI0939JLGV/@@download/IGVFFI0939JLGV.fastq.gz",
"md5sum": "f880147b17ff2894dcab45d9036e835b",
"s3_uri": "s3://igvf-files/2024/06/01/b1a72dd0-952b-485b-87cd-048609254313/IGVFFI0939JLGV.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-BinF-PCR2_S174_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": "2024-07-10T19:49:48.700268+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4674ZTIR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4674ZTIR",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR1_S78",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR2_S174",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR3_S270",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin0hrs-FF1-BinF-PCR4_S366"
],
"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 F for 80-100% 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": "2024-06-01T01:29:25.532695+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": "2ec3873a-f7fc-420c-a716-7693a8c95bfb"
}