{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6901XNIT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6901XNIT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198"
],
"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": "In vitro system [IGVFSM2608ULOG](/in-vitro-systems/IGVFSM2608ULOG/) 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/IGVFSM2608ULOG/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6901XNIT](/measurement-sets/IGVFDS6901XNIT/) 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/IGVFDS6901XNIT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6901XNIT](/measurement-sets/IGVFDS6901XNIT/) has sequence file(s) [IGVFFI3818YHBA](/sequence-files/IGVFFI3818YHBA/), [IGVFFI1752SCWZ](/sequence-files/IGVFFI1752SCWZ/), [IGVFFI9374WFBZ](/sequence-files/IGVFFI9374WFBZ/), [IGVFFI7816MRXM](/sequence-files/IGVFFI7816MRXM/) 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/IGVFDS6901XNIT/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS9190KTAF](/auxiliary-sets/IGVFDS9190KTAF/) 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/IGVFDS9190KTAF/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2608ULOG](/in-vitro-systems/IGVFSM2608ULOG/) 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/IGVFSM2608ULOG/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9190KTAF/",
"accession": "IGVFDS9190KTAF",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_FAM3C_Auxin6hrs-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/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": "2024-05-14T16:41:43.093614+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/IGVFFI9937DSFB/",
"accession": "IGVFFI9937DSFB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:07.097511+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9937DSFB/@@download/IGVFFI9937DSFB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b74160f4-3c6a-472b-91b1-22e773e8ca36/IGVFFI9937DSFB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4905OMVY/",
"accession": "IGVFFI4905OMVY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:34.348780+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI4905OMVY/@@download/IGVFFI4905OMVY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f96e0a29-b9a3-4db4-83ce-4cfa5f74bcf5/IGVFFI4905OMVY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9544ZFOX/",
"accession": "IGVFFI9544ZFOX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:20.711049+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9544ZFOX/@@download/IGVFFI9544ZFOX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/94376427-aae2-4c25-84a7-26dc4dbfc78a/IGVFFI9544ZFOX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7297AXPH/",
"accession": "IGVFFI7297AXPH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:53.179370+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI7297AXPH/@@download/IGVFFI7297AXPH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e1ec87eb-050f-4ece-9111-8414c0918e04/IGVFFI7297AXPH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3818YHBA/",
"accession": "IGVFFI3818YHBA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:11.574431+00:00",
"file_format": "fastq",
"file_size": 40722441,
"href": "/sequence-files/IGVFFI3818YHBA/@@download/IGVFFI3818YHBA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8c6a0beb-9d37-43ce-83a5-1db0959216ff/IGVFFI3818YHBA.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-Auxin6hrs-FF1-BinF-PCR3-Rep1_S192_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1752SCWZ/",
"accession": "IGVFFI1752SCWZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:30.207058+00:00",
"file_format": "fastq",
"file_size": 32574355,
"href": "/sequence-files/IGVFFI1752SCWZ/@@download/IGVFFI1752SCWZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/019c02f8-1822-4efd-a61a-7fd46a28d45a/IGVFFI1752SCWZ.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-Auxin6hrs-FF1-BinF-PCR4-Rep1_S198_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9374WFBZ/",
"accession": "IGVFFI9374WFBZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:34.859990+00:00",
"file_format": "fastq",
"file_size": 28163239,
"href": "/sequence-files/IGVFFI9374WFBZ/@@download/IGVFFI9374WFBZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/225ff9a4-28e1-4528-9531-4e776bd7ab34/IGVFFI9374WFBZ.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-Auxin6hrs-FF1-BinF-PCR1-Rep1_S138_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7816MRXM/",
"accession": "IGVFFI7816MRXM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:53.150402+00:00",
"file_format": "fastq",
"file_size": 24050486,
"href": "/sequence-files/IGVFFI7816MRXM/@@download/IGVFFI7816MRXM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7aff82f3-ee66-4bdf-9fd7-ce0a3eb7cc8b/IGVFFI7816MRXM.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-Auxin6hrs-FF1-BinF-PCR2-Rep1_S144_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": "2024-07-10T19:41:12.445171+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2608ULOG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2608ULOG",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR1-Rep1_S138",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR2-Rep1_S144",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR3-Rep1_S192",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinF-PCR4-Rep1_S198"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"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 FAM3C) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:53:34.859990+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": "08d7df66-74f5-4baf-adc5-ed9f3dd360d6"
}