{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9829XFGT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9829XFGT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184"
],
"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": "In vitro system [IGVFSM8987EBZC](/in-vitro-systems/IGVFSM8987EBZC/) 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/IGVFSM8987EBZC/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9829XFGT](/measurement-sets/IGVFDS9829XFGT/) 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/IGVFDS9829XFGT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9829XFGT](/measurement-sets/IGVFDS9829XFGT/) has sequence file(s) [IGVFFI4287HCJU](/sequence-files/IGVFFI4287HCJU/), [IGVFFI0373YORO](/sequence-files/IGVFFI0373YORO/), [IGVFFI8597VYJU](/sequence-files/IGVFFI8597VYJU/), [IGVFFI7926SPBK](/sequence-files/IGVFFI7926SPBK/) 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/IGVFDS9829XFGT/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8987EBZC](/in-vitro-systems/IGVFSM8987EBZC/) 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/IGVFSM8987EBZC/"
}
]
},
"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": "2024-05-14T16:16:39.023952+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/IGVFFI1867PKWL/",
"accession": "IGVFFI1867PKWL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:06.899323+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1867PKWL/@@download/IGVFFI1867PKWL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8eabee1f-c0fd-48f8-9a8b-90f66dbc327c/IGVFFI1867PKWL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4287HCJU/",
"accession": "IGVFFI4287HCJU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:52:52.381866+00:00",
"file_format": "fastq",
"file_size": 32929762,
"href": "/sequence-files/IGVFFI4287HCJU/@@download/IGVFFI4287HCJU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/990d8a43-ee13-4bd8-9b16-99a9e003ad71/IGVFFI4287HCJU.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-BinD-PCR3-Rep1_S178_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9134XSQU/",
"accession": "IGVFFI9134XSQU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:21.005310+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9134XSQU/@@download/IGVFFI9134XSQU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9afd181f-bd31-482b-91ef-a3b463b200ec/IGVFFI9134XSQU.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7940UOBI/",
"accession": "IGVFFI7940UOBI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:53.157858+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI7940UOBI/@@download/IGVFFI7940UOBI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/44aa4f54-4f71-4087-ac17-93b46f059102/IGVFFI7940UOBI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0373YORO/",
"accession": "IGVFFI0373YORO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:52:34.018365+00:00",
"file_format": "fastq",
"file_size": 23437372,
"href": "/sequence-files/IGVFFI0373YORO/@@download/IGVFFI0373YORO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/55bd388c-a640-4ea8-9f46-1a53592b9a56/IGVFFI0373YORO.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-BinD-PCR2-Rep1_S130_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9099WRSF/",
"accession": "IGVFFI9099WRSF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:34.301011+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9099WRSF/@@download/IGVFFI9099WRSF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1a81be6e-4613-4146-9c8d-f7631c0b9eaf/IGVFFI9099WRSF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8597VYJU/",
"accession": "IGVFFI8597VYJU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:52:16.243482+00:00",
"file_format": "fastq",
"file_size": 23768552,
"href": "/sequence-files/IGVFFI8597VYJU/@@download/IGVFFI8597VYJU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/dfa45282-1f3d-4b22-824e-d6e8696f0558/IGVFFI8597VYJU.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-BinD-PCR1-Rep1_S124_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7926SPBK/",
"accession": "IGVFFI7926SPBK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:10.393973+00:00",
"file_format": "fastq",
"file_size": 35216637,
"href": "/sequence-files/IGVFFI7926SPBK/@@download/IGVFFI7926SPBK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fafde862-bed5-44fb-8bc2-5cfb8612577f/IGVFFI7926SPBK.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-BinD-PCR4-Rep1_S184_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": "2024-07-10T19:40:33.619227+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8987EBZC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8987EBZC",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR1-Rep1_S124",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR2-Rep1_S130",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR3-Rep1_S178",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinD-PCR4-Rep1_S184"
],
"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 D for 55-65% 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": "2024-06-01T01:52:16.243482+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": "7eb200a7-c13d-4a26-9b72-7dfdd79cb000"
}