{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6376TFTJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6376TFTJ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
],
"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 [IGVFDS6376TFTJ](/measurement-sets/IGVFDS6376TFTJ/) links to sample [IGVFSM9315IOJD](/in-vitro-systems/IGVFSM9315IOJD/) which links to auxiliary set [IGVFDS5464XLTY](/auxiliary-sets/IGVFDS5464XLTY/) 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/IGVFDS6376TFTJ/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6376TFTJ](/measurement-sets/IGVFDS6376TFTJ/) 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/IGVFDS6376TFTJ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6376TFTJ](/measurement-sets/IGVFDS6376TFTJ/) has sequence file(s) [IGVFFI1384RCQE](/sequence-files/IGVFFI1384RCQE/), [IGVFFI4291ESKX](/sequence-files/IGVFFI4291ESKX/), [IGVFFI3927LCXN](/sequence-files/IGVFFI3927LCXN/), [IGVFFI8797POIP](/sequence-files/IGVFFI8797POIP/) 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/IGVFDS6376TFTJ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6376TFTJ](/measurement-sets/IGVFDS6376TFTJ/) has revoked subobject auxiliary set [IGVFDS0319JZYS](/auxiliary-sets/IGVFDS0319JZYS/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6376TFTJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9315IOJD](/in-vitro-systems/IGVFSM9315IOJD/) 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/IGVFSM9315IOJD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Auxiliary set [IGVFDS0319JZYS](/auxiliary-sets/IGVFDS0319JZYS/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/auxiliary-sets/IGVFDS0319JZYS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6376TFTJ](/measurement-sets/IGVFDS6376TFTJ/) 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/IGVFDS6376TFTJ/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9315IOJD](/in-vitro-systems/IGVFSM9315IOJD/) 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/IGVFSM9315IOJD/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0319JZYS/",
"accession": "IGVFDS0319JZYS",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
],
"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/IGVFDS6351FGNG/",
"accession": "IGVFDS6351FGNG",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5924HOIN/",
"accession": "IGVFFI5924HOIN",
"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": "2024-05-13T22:07:21.499963+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/IGVFFI6982FUBD/",
"accession": "IGVFFI6982FUBD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:41.197659+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI6982FUBD/@@download/IGVFFI6982FUBD.yaml.gz",
"md5sum": "b8974b9aeec5a1c5ecbfb9adbc63dafe",
"s3_uri": "s3://igvf-files/2024/06/11/bb8c1480-e476-44f4-b97a-283171c69696/IGVFFI6982FUBD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1384RCQE/",
"accession": "IGVFFI1384RCQE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:50.518482+00:00",
"file_format": "fastq",
"file_size": 25189873,
"href": "/sequence-files/IGVFFI1384RCQE/@@download/IGVFFI1384RCQE.fastq.gz",
"md5sum": "84319a105132b60b1fbe737279451a74",
"s3_uri": "s3://igvf-files/2024/06/01/212cfb93-8307-4575-8e5e-083217bd59cf/IGVFFI1384RCQE.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/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR4-Rep1_S265_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1446IYEI/",
"accession": "IGVFFI1446IYEI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:12.941557+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI1446IYEI/@@download/IGVFFI1446IYEI.yaml.gz",
"md5sum": "505a821d565566f25d0d6b908c241a8d",
"s3_uri": "s3://igvf-files/2024/06/11/1ff34b94-983c-44a7-b74f-1c3f9bf4f549/IGVFFI1446IYEI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0717WSTW/",
"accession": "IGVFFI0717WSTW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:28:27.403902+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI0717WSTW/@@download/IGVFFI0717WSTW.yaml.gz",
"md5sum": "750c906d643bc553fc61e0bba4bae3d7",
"s3_uri": "s3://igvf-files/2024/06/11/5c6165a7-3847-4a1f-8f27-b75bc7601575/IGVFFI0717WSTW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4291ESKX/",
"accession": "IGVFFI4291ESKX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:32.542392+00:00",
"file_format": "fastq",
"file_size": 30283642,
"href": "/sequence-files/IGVFFI4291ESKX/@@download/IGVFFI4291ESKX.fastq.gz",
"md5sum": "05baecd4876ad2ab1d5dcf5ec764fd7a",
"s3_uri": "s3://igvf-files/2024/06/01/b769cc3d-84cf-41f6-9373-6090410687f7/IGVFFI4291ESKX.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/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR3-Rep1_S259_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7867OONC/",
"accession": "IGVFFI7867OONC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:27:58.294046+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7867OONC/@@download/IGVFFI7867OONC.yaml.gz",
"md5sum": "de49424f4edb1a2e576879242de75515",
"s3_uri": "s3://igvf-files/2024/06/11/930f1b1a-12c6-4d25-9491-84f6828579cc/IGVFFI7867OONC.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3927LCXN/",
"accession": "IGVFFI3927LCXN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:35:55.762873+00:00",
"file_format": "fastq",
"file_size": 22496682,
"href": "/sequence-files/IGVFFI3927LCXN/@@download/IGVFFI3927LCXN.fastq.gz",
"md5sum": "507bc449bae872df84a06f30b1bb77a3",
"s3_uri": "s3://igvf-files/2024/06/01/dfc39d1a-e2e6-44b3-863e-d2f3b4958692/IGVFFI3927LCXN.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/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR1-Rep1_S217_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8797POIP/",
"accession": "IGVFFI8797POIP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:36:14.278905+00:00",
"file_format": "fastq",
"file_size": 17334895,
"href": "/sequence-files/IGVFFI8797POIP/@@download/IGVFFI8797POIP.fastq.gz",
"md5sum": "8d986110932c24625d57e0a4f6671a92",
"s3_uri": "s3://igvf-files/2024/06/01/d9548d5b-ab17-4c0b-a5f1-c8b0529d7616/IGVFFI8797POIP.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/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF1-BinA-PCR2-Rep1_S223_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"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": "2024-07-10T19:37:41.161637+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9315IOJD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9315IOJD",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR1-Rep1_S217",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR2-Rep1_S223",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR3-Rep1_S259",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinA-PCR4-Rep1_S265"
],
"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 A for 0-10% 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": "2024-06-01T01:35:55.762873+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of CCND1 integrating a guide (sgRNA) library targeting accessible genome regions in many 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": "a1ccc6cc-d9a8-4e7b-ae1a-1da5a7d76123"
}