{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2315UDUR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2315UDUR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"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 [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/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2315UDUR](/measurement-sets/IGVFDS2315UDUR/) 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/IGVFDS2315UDUR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2315UDUR](/measurement-sets/IGVFDS2315UDUR/) has sequence file(s) [IGVFFI0003GKTA](/sequence-files/IGVFFI0003GKTA/), [IGVFFI5753MODI](/sequence-files/IGVFFI5753MODI/), [IGVFFI8644ELSX](/sequence-files/IGVFFI8644ELSX/), [IGVFFI8303KMQH](/sequence-files/IGVFFI8303KMQH/) 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/IGVFDS2315UDUR/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6928JPHO](/in-vitro-systems/IGVFSM6928JPHO/) 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/IGVFSM6928JPHO/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6928JPHO](/in-vitro-systems/IGVFSM6928JPHO/) 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/IGVFSM6928JPHO/"
}
]
},
"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": "2024-05-14T16:41:39.101161+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/IGVFFI9546POQT/",
"accession": "IGVFFI9546POQT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:02.557487+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI9546POQT/@@download/IGVFFI9546POQT.yaml.gz",
"md5sum": "b4e3d7a2e6ba1f2c5cddaee8fe7ca25c",
"s3_uri": "s3://igvf-files/2024/06/11/b699eadb-d44c-42db-a9c7-a696db179ec6/IGVFFI9546POQT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2872OELQ/",
"accession": "IGVFFI2872OELQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:48.524116+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2872OELQ/@@download/IGVFFI2872OELQ.yaml.gz",
"md5sum": "092651a392d7002f860fed3874ac619a",
"s3_uri": "s3://igvf-files/2024/06/11/2a932c52-0b85-415b-a7e1-0023b54fcf03/IGVFFI2872OELQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0910MBLA/",
"accession": "IGVFFI0910MBLA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:29.977867+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI0910MBLA/@@download/IGVFFI0910MBLA.yaml.gz",
"md5sum": "1fd190e728728f22cd6f8fa058ca1bef",
"s3_uri": "s3://igvf-files/2024/06/11/15103a88-96d8-494c-a62b-4372c55c5801/IGVFFI0910MBLA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0003GKTA/",
"accession": "IGVFFI0003GKTA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:24.045661+00:00",
"file_format": "fastq",
"file_size": 27878556,
"href": "/sequence-files/IGVFFI0003GKTA/@@download/IGVFFI0003GKTA.fastq.gz",
"md5sum": "14b3a12169f80c5812db09833f8ad69a",
"s3_uri": "s3://igvf-files/2024/06/01/3ced79d6-a73c-471f-a681-db8b71db0241/IGVFFI0003GKTA.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-BinD-PCR4-Rep1_S196_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6470EGGF/",
"accession": "IGVFFI6470EGGF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:16.301247+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI6470EGGF/@@download/IGVFFI6470EGGF.yaml.gz",
"md5sum": "29dac97c7931c8a92262697f2dad16c1",
"s3_uri": "s3://igvf-files/2024/06/11/4bf8edef-bc26-4857-ad1f-6a0a5732f3ff/IGVFFI6470EGGF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5753MODI/",
"accession": "IGVFFI5753MODI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:47.027427+00:00",
"file_format": "fastq",
"file_size": 16779582,
"href": "/sequence-files/IGVFFI5753MODI/@@download/IGVFFI5753MODI.fastq.gz",
"md5sum": "1b361ba8f6081505ccf0d0aaaf16159a",
"s3_uri": "s3://igvf-files/2024/06/01/a4b41623-608e-4802-b8ef-44b046dd49cb/IGVFFI5753MODI.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-BinD-PCR2-Rep1_S142_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8644ELSX/",
"accession": "IGVFFI8644ELSX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:28.759279+00:00",
"file_format": "fastq",
"file_size": 23487754,
"href": "/sequence-files/IGVFFI8644ELSX/@@download/IGVFFI8644ELSX.fastq.gz",
"md5sum": "75d3e9561ce27b8f5f93399593dc1374",
"s3_uri": "s3://igvf-files/2024/06/01/13ee86c5-a85b-4fc0-be0b-9775e621b630/IGVFFI8644ELSX.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-BinD-PCR1-Rep1_S136_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8303KMQH/",
"accession": "IGVFFI8303KMQH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:54:05.364093+00:00",
"file_format": "fastq",
"file_size": 31644031,
"href": "/sequence-files/IGVFFI8303KMQH/@@download/IGVFFI8303KMQH.fastq.gz",
"md5sum": "f926deae685f2987cbb18fff24564fe1",
"s3_uri": "s3://igvf-files/2024/06/01/aeebe66c-e6a6-493d-bb62-4c4b8cc7af8f/IGVFFI8303KMQH.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-BinD-PCR3-Rep1_S190_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": "2024-07-10T19:41:00.384678+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6928JPHO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6928JPHO",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"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 D for 55-65% 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": "2024-06-01T01:53:28.759279+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": "531717d0-866a-48cd-8091-bc306fba24ce"
}