{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6663FDTV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6663FDTV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
],
"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": "Auxiliary set [IGVFDS0713EITK](/auxiliary-sets/IGVFDS0713EITK/) 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/IGVFDS0713EITK/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6663FDTV](/measurement-sets/IGVFDS6663FDTV/) 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/IGVFDS6663FDTV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6663FDTV](/measurement-sets/IGVFDS6663FDTV/) has sequence file(s) [IGVFFI0237YEQF](/sequence-files/IGVFFI0237YEQF/), [IGVFFI5330ZBZF](/sequence-files/IGVFFI5330ZBZF/), [IGVFFI4161WIYC](/sequence-files/IGVFFI4161WIYC/), [IGVFFI6786VTNX](/sequence-files/IGVFFI6786VTNX/) 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/IGVFDS6663FDTV/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3569TFCR](/in-vitro-systems/IGVFSM3569TFCR/) 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/IGVFSM3569TFCR/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3569TFCR](/in-vitro-systems/IGVFSM3569TFCR/) 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/IGVFSM3569TFCR/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0713EITK/",
"accession": "IGVFDS0713EITK",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_FAM3C_Auxin0hrs-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/IGVFDS1891GTLU/",
"accession": "IGVFDS1891GTLU",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI0842RREU/",
"accession": "IGVFFI0842RREU",
"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": "2024-05-14T16:16:37.246300+00:00",
"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/IGVFFI8739NONQ/",
"accession": "IGVFFI8739NONQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:48.825129+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8739NONQ/@@download/IGVFFI8739NONQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7595ec06-0f54-482c-b261-4e4b14f7e418/IGVFFI8739NONQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3135DSDD/",
"accession": "IGVFFI3135DSDD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:29.934271+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI3135DSDD/@@download/IGVFFI3135DSDD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0388b421-978f-4f84-8334-ad3fe4bad3ff/IGVFFI3135DSDD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI5430OQAY/",
"accession": "IGVFFI5430OQAY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:16.719372+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5430OQAY/@@download/IGVFFI5430OQAY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/09445a76-3b78-40eb-be23-6ea949669e94/IGVFFI5430OQAY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2775UGHY/",
"accession": "IGVFFI2775UGHY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:02.488282+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2775UGHY/@@download/IGVFFI2775UGHY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/36624d58-64f2-4f30-b001-49115769d501/IGVFFI2775UGHY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0237YEQF/",
"accession": "IGVFFI0237YEQF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:04.498696+00:00",
"file_format": "fastq",
"file_size": 22293288,
"href": "/sequence-files/IGVFFI0237YEQF/@@download/IGVFFI0237YEQF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/4793a8ad-18c3-4cac-8b3e-56c405d82d32/IGVFFI0237YEQF.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/FAM3C-Auxin0hrs-FF2-BinB-PCR4-Rep1_S182_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5330ZBZF/",
"accession": "IGVFFI5330ZBZF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:52:28.220317+00:00",
"file_format": "fastq",
"file_size": 13261753,
"href": "/sequence-files/IGVFFI5330ZBZF/@@download/IGVFFI5330ZBZF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/eb458fc3-1f12-4329-b7b5-59f39c61c0e8/IGVFFI5330ZBZF.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/FAM3C-Auxin0hrs-FF2-BinB-PCR2-Rep1_S128_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4161WIYC/",
"accession": "IGVFFI4161WIYC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:52:09.910992+00:00",
"file_format": "fastq",
"file_size": 15031923,
"href": "/sequence-files/IGVFFI4161WIYC/@@download/IGVFFI4161WIYC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a3a66435-bad2-4ea4-b510-e3a7709e76a4/IGVFFI4161WIYC.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/FAM3C-Auxin0hrs-FF2-BinB-PCR1-Rep1_S122_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6786VTNX/",
"accession": "IGVFFI6786VTNX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:52:46.255837+00:00",
"file_format": "fastq",
"file_size": 25060691,
"href": "/sequence-files/IGVFFI6786VTNX/@@download/IGVFFI6786VTNX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e342dd20-bb98-4939-9231-6fb3157dd5a0/IGVFFI6786VTNX.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/FAM3C-Auxin0hrs-FF2-BinB-PCR3-Rep1_S176_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5239VQTN/"
],
"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": "2024-07-10T19:40:25.537998+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3569TFCR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3569TFCR",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR1-Rep1_S122",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR2-Rep1_S128",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR3-Rep1_S176",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinB-PCR4-Rep1_S182"
],
"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 FAM3C) 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": "2024-06-01T01:52:09.910992+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of FAM3C integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000196937/",
"geneid": "ENSG00000196937",
"name": "FAM3 metabolism regulating signaling molecule C",
"status": "released",
"symbol": "FAM3C",
"synonyms": [
"FAM3 metabolism regulating signaling molecule C",
"FAM3C",
"interleukin-like EMT inducer",
"protein FAM3C",
"predicted osteoblast protein",
"family with sequence similarity 3 member C",
"ILEI",
"GS3786",
"interleukin-like epithelial-mesenchymal transition inducer"
]
}
],
"uuid": "3d0e5441-4404-4bd1-950a-76d7add5e4fe"
}