{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9034AAFA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9034AAFA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210"
],
"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 [IGVFDS0422FVNU](/auxiliary-sets/IGVFDS0422FVNU/) 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/IGVFDS0422FVNU/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2356KPRX](/in-vitro-systems/IGVFSM2356KPRX/) 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/IGVFSM2356KPRX/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9034AAFA](/measurement-sets/IGVFDS9034AAFA/) 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/IGVFDS9034AAFA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9034AAFA](/measurement-sets/IGVFDS9034AAFA/) has sequence file(s) [IGVFFI8480BRGG](/sequence-files/IGVFFI8480BRGG/), [IGVFFI8430IXFV](/sequence-files/IGVFFI8430IXFV/), [IGVFFI8181DYGV](/sequence-files/IGVFFI8181DYGV/), [IGVFFI8166TMOU](/sequence-files/IGVFFI8166TMOU/) 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/IGVFDS9034AAFA/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2356KPRX](/in-vitro-systems/IGVFSM2356KPRX/) 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/IGVFSM2356KPRX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0422FVNU/",
"accession": "IGVFDS0422FVNU",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_FAM3C_Auxin6hrs-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": "2024-05-14T16:42:05.370141+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/IGVFFI7169ITED/",
"accession": "IGVFFI7169ITED",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:02.917201+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI7169ITED/@@download/IGVFFI7169ITED.yaml.gz",
"md5sum": "a02531984533af7c15d70157d20bce20",
"s3_uri": "s3://igvf-files/2024/06/11/460cf5f8-1f19-467d-ba50-b94583531ab9/IGVFFI7169ITED.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4656ZGKK/",
"accession": "IGVFFI4656ZGKK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:30.021186+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4656ZGKK/@@download/IGVFFI4656ZGKK.yaml.gz",
"md5sum": "702bf5cb0c77fb2c2bcf26540b94677e",
"s3_uri": "s3://igvf-files/2024/06/11/6f1581a4-eead-4e95-ad5c-a0bd6e7c7d7f/IGVFFI4656ZGKK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0106NXXW/",
"accession": "IGVFFI0106NXXW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:16.410462+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0106NXXW/@@download/IGVFFI0106NXXW.yaml.gz",
"md5sum": "6cc3896b69720fb686c87bc166870bc9",
"s3_uri": "s3://igvf-files/2024/06/11/43a4486b-126b-4e51-92f0-53c7dfc11e07/IGVFFI0106NXXW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8480BRGG/",
"accession": "IGVFFI8480BRGG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:55:06.412526+00:00",
"file_format": "fastq",
"file_size": 16085143,
"href": "/sequence-files/IGVFFI8480BRGG/@@download/IGVFFI8480BRGG.fastq.gz",
"md5sum": "f6bb198432486427b8af2a97dc9c97d3",
"s3_uri": "s3://igvf-files/2024/06/01/3e117dc8-971b-4ddc-97bd-1ee7cdc7286e/IGVFFI8480BRGG.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-FF2-BinF-PCR2-Rep1_S156_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9000DITZ/",
"accession": "IGVFFI9000DITZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:49.239577+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI9000DITZ/@@download/IGVFFI9000DITZ.yaml.gz",
"md5sum": "09bf3995508c4a88e90001df95fd5194",
"s3_uri": "s3://igvf-files/2024/06/11/fb6a6dbe-0b76-4c8f-92be-a3c2edc2473e/IGVFFI9000DITZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8430IXFV/",
"accession": "IGVFFI8430IXFV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:48.144894+00:00",
"file_format": "fastq",
"file_size": 18316143,
"href": "/sequence-files/IGVFFI8430IXFV/@@download/IGVFFI8430IXFV.fastq.gz",
"md5sum": "ce8053dedfa5cfb7bdcb8ab62ce74e40",
"s3_uri": "s3://igvf-files/2024/06/01/9b68bd2a-7f05-4533-a071-3bf5fb2eb277/IGVFFI8430IXFV.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-FF2-BinF-PCR1-Rep1_S150_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8181DYGV/",
"accession": "IGVFFI8181DYGV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:55:42.856384+00:00",
"file_format": "fastq",
"file_size": 27609239,
"href": "/sequence-files/IGVFFI8181DYGV/@@download/IGVFFI8181DYGV.fastq.gz",
"md5sum": "0c3c5dddfd8b405ce0f9787b69eb0da4",
"s3_uri": "s3://igvf-files/2024/06/01/a4f31601-64b2-4549-8313-0ce6b6dbe4fc/IGVFFI8181DYGV.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-FF2-BinF-PCR4-Rep1_S210_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8166TMOU/",
"accession": "IGVFFI8166TMOU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:55:24.930504+00:00",
"file_format": "fastq",
"file_size": 26219982,
"href": "/sequence-files/IGVFFI8166TMOU/@@download/IGVFFI8166TMOU.fastq.gz",
"md5sum": "c12c35ad099e1ca5adc0afb5726505fe",
"s3_uri": "s3://igvf-files/2024/06/01/95d24e65-7d4b-4d9e-9668-a2d72c401e9f/IGVFFI8166TMOU.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-FF2-BinF-PCR3-Rep1_S204_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": "2024-07-10T19:41:47.033307+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2356KPRX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2356KPRX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR1-Rep1_S150",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR2-Rep1_S156",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR3-Rep1_S204",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF2-BinF-PCR4-Rep1_S210"
],
"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_term_name": "5-Phenyl-1H-indole-3-acetic acid",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:54:48.144894+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": "0c4f75f0-a05b-40f4-9f86-46b002b66544"
}