{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3995SYLS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3995SYLS",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186"
],
"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": "Measurement set [IGVFDS3995SYLS](/measurement-sets/IGVFDS3995SYLS/) 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/IGVFDS3995SYLS/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3995SYLS](/measurement-sets/IGVFDS3995SYLS/) has sequence file(s) [IGVFFI7793HRXV](/sequence-files/IGVFFI7793HRXV/), [IGVFFI7085ICFZ](/sequence-files/IGVFFI7085ICFZ/), [IGVFFI6643LUII](/sequence-files/IGVFFI6643LUII/), [IGVFFI3507JHKO](/sequence-files/IGVFFI3507JHKO/) 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/IGVFDS3995SYLS/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4323ZIMC](/in-vitro-systems/IGVFSM4323ZIMC/) 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/IGVFSM4323ZIMC/"
},
{
"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/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM4323ZIMC](/in-vitro-systems/IGVFSM4323ZIMC/) 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/IGVFSM4323ZIMC/"
}
]
},
"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": "2024-05-14T16:16:40.563131+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/IGVFFI4303KRTG/",
"accession": "IGVFFI4303KRTG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:57.683626+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4303KRTG/@@download/IGVFFI4303KRTG.yaml.gz",
"md5sum": "4e76f8ac8ff3342a1afd1e81792ee914",
"s3_uri": "s3://igvf-files/2024/06/11/7d215708-2e67-4035-9005-c3c1cd87e75b/IGVFFI4303KRTG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7793HRXV/",
"accession": "IGVFFI7793HRXV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:52:40.154073+00:00",
"file_format": "fastq",
"file_size": 23971288,
"href": "/sequence-files/IGVFFI7793HRXV/@@download/IGVFFI7793HRXV.fastq.gz",
"md5sum": "5c2e194adaf51bfb333d95fa060d3791",
"s3_uri": "s3://igvf-files/2024/06/01/93f01b58-212d-4652-afa9-97427055093b/IGVFFI7793HRXV.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-BinF-PCR2-Rep1_S132_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3932WMWI/",
"accession": "IGVFFI3932WMWI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:38.811632+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI3932WMWI/@@download/IGVFFI3932WMWI.yaml.gz",
"md5sum": "ac370da6bfe3819150a18108828f8579",
"s3_uri": "s3://igvf-files/2024/06/11/87a4dced-a321-4a90-8da4-5df3bf1e97df/IGVFFI3932WMWI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4738IQYH/",
"accession": "IGVFFI4738IQYH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:25.494746+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4738IQYH/@@download/IGVFFI4738IQYH.yaml.gz",
"md5sum": "789860b9107a4120a765249ada9a8c12",
"s3_uri": "s3://igvf-files/2024/06/11/8571ecc5-225b-4798-881a-2756020ef298/IGVFFI4738IQYH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8140XRRA/",
"accession": "IGVFFI8140XRRA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:11.341753+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8140XRRA/@@download/IGVFFI8140XRRA.yaml.gz",
"md5sum": "0f42eea3570eaf5e905e182596a6d834",
"s3_uri": "s3://igvf-files/2024/06/11/4013fc4c-6be8-4b7c-9c29-460520200fd8/IGVFFI8140XRRA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI7085ICFZ/",
"accession": "IGVFFI7085ICFZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:52:58.282324+00:00",
"file_format": "fastq",
"file_size": 41969951,
"href": "/sequence-files/IGVFFI7085ICFZ/@@download/IGVFFI7085ICFZ.fastq.gz",
"md5sum": "8f395653dd9e47ec93e9cb7ea12cc4fd",
"s3_uri": "s3://igvf-files/2024/06/01/8014f949-476d-4628-a8e7-178340dcec94/IGVFFI7085ICFZ.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-BinF-PCR3-Rep1_S180_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6643LUII/",
"accession": "IGVFFI6643LUII",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:53:16.566885+00:00",
"file_format": "fastq",
"file_size": 30536690,
"href": "/sequence-files/IGVFFI6643LUII/@@download/IGVFFI6643LUII.fastq.gz",
"md5sum": "c3c7a0a6e3da38eb62e367cf46b2d2aa",
"s3_uri": "s3://igvf-files/2024/06/01/15dbd0ea-a7d0-4093-8160-efb21ec17d0f/IGVFFI6643LUII.fastq.gz",
"sequencing_platform": {
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"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-BinF-PCR4-Rep1_S186_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3507JHKO/",
"accession": "IGVFFI3507JHKO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:52:22.104712+00:00",
"file_format": "fastq",
"file_size": 28778627,
"href": "/sequence-files/IGVFFI3507JHKO/@@download/IGVFFI3507JHKO.fastq.gz",
"md5sum": "f435f42ff7cc4f0db70b1fac8b483265",
"s3_uri": "s3://igvf-files/2024/06/01/e6f663bf-0cf0-4839-8c91-944914fbd759/IGVFFI3507JHKO.fastq.gz",
"sequencing_platform": {
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"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-BinF-PCR1-Rep1_S126_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": "2024-07-10T19:40:41.708751+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4323ZIMC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4323ZIMC",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR1-Rep1_S126",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR2-Rep1_S132",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR3-Rep1_S180",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinF-PCR4-Rep1_S186"
],
"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 F for 80-100% 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": "2024-06-01T01:52:22.104712+00:00",
"summary": " 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": "bc0ec689-ef4a-4af1-a24d-3866b743bf24"
}