{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0674KOZU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0674KOZU",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"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 [IGVFDS0674KOZU](/measurement-sets/IGVFDS0674KOZU/) 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/IGVFDS0674KOZU/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0674KOZU](/measurement-sets/IGVFDS0674KOZU/) has sequence file(s) [IGVFFI9696NSTM](/sequence-files/IGVFFI9696NSTM/), [IGVFFI8263MWWS](/sequence-files/IGVFFI8263MWWS/), [IGVFFI3575WNTZ](/sequence-files/IGVFFI3575WNTZ/), [IGVFFI1019WGYS](/sequence-files/IGVFFI1019WGYS/) 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/IGVFDS0674KOZU/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS1546MEZJ](/auxiliary-sets/IGVFDS1546MEZJ/) 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/IGVFDS1546MEZJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4326ZGNE](/in-vitro-systems/IGVFSM4326ZGNE/) 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/IGVFSM4326ZGNE/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM4326ZGNE](/in-vitro-systems/IGVFSM4326ZGNE/) 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/IGVFSM4326ZGNE/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1546MEZJ/",
"accession": "IGVFDS1546MEZJ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_SSFA2-Auxin0hrs-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/IGVFDS5413RKIA/",
"accession": "IGVFDS5413RKIA",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5130EWUZ/",
"accession": "IGVFFI5130EWUZ",
"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": "2024-05-14T20:32:56.216811+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/IGVFFI8013LHCK/",
"accession": "IGVFFI8013LHCK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:59.510511+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8013LHCK/@@download/IGVFFI8013LHCK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3dcfa6d0-8d12-4599-ad28-bd5a6a274728/IGVFFI8013LHCK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9696NSTM/",
"accession": "IGVFFI9696NSTM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:45:44.683382+00:00",
"file_format": "fastq",
"file_size": 24887465,
"href": "/sequence-files/IGVFFI9696NSTM/@@download/IGVFFI9696NSTM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e87543cb-09a8-41be-9333-8f0db40080d6/IGVFFI9696NSTM.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/SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5738MQSZ/",
"accession": "IGVFFI5738MQSZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:29.158263+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5738MQSZ/@@download/IGVFFI5738MQSZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f7f901d8-d2e9-42c6-82d0-51f2cce9a8b0/IGVFFI5738MQSZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI8263MWWS/",
"accession": "IGVFFI8263MWWS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:45:09.229837+00:00",
"file_format": "fastq",
"file_size": 35207176,
"href": "/sequence-files/IGVFFI8263MWWS/@@download/IGVFFI8263MWWS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/bd0e67cf-a11f-413e-8b04-c75912dd7f59/IGVFFI8263MWWS.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/SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5161XQVK/",
"accession": "IGVFFI5161XQVK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:44.068688+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5161XQVK/@@download/IGVFFI5161XQVK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/62ede40d-3c8a-440b-a003-7570bfc03728/IGVFFI5161XQVK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3575WNTZ/",
"accession": "IGVFFI3575WNTZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:45:26.802479+00:00",
"file_format": "fastq",
"file_size": 27117255,
"href": "/sequence-files/IGVFFI3575WNTZ/@@download/IGVFFI3575WNTZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3aeb7dac-ca1b-42a4-9d93-933052b2d191/IGVFFI3575WNTZ.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/SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3817IEYP/",
"accession": "IGVFFI3817IEYP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:15.142296+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI3817IEYP/@@download/IGVFFI3817IEYP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/00f9a3e6-6de5-4623-a80e-7ececd0a32cc/IGVFFI3817IEYP.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1019WGYS/",
"accession": "IGVFFI1019WGYS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:44:50.372423+00:00",
"file_format": "fastq",
"file_size": 29169256,
"href": "/sequence-files/IGVFFI1019WGYS/@@download/IGVFFI1019WGYS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6a0ef93b-d83f-43b4-84e3-f59c08f4fed4/IGVFFI1019WGYS.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/SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2031CTSP/"
],
"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": "2024-07-10T19:51:18.436258+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4326ZGNE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4326ZGNE",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR3-Rep1_S60",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinF-PCR4-Rep1_S66"
],
"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 SSFA2) 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": "2024-06-01T01:44:50.372423+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of ITPRID2 integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000138434/",
"geneid": "ENSG00000138434",
"name": "ITPR interacting domain containing 2",
"status": "released",
"symbol": "ITPRID2",
"synonyms": [
"sperm associated antigen 13",
"ITPR interacting domain containing 2",
"ITPR-interacting domain-containing protein 2",
"SSFA2",
"KRAS-induced actin-interacting protein",
"cleavage signal-1 protein",
"ki-ras-induced actin-interacting protein",
"sperm specific antigen 2",
"ITPRID2",
"SPAG13",
"protein ITPRID2",
"CS-1",
"CS1",
"KRAP"
]
}
],
"uuid": "867c79de-43da-46e2-abcf-0dddb746e612"
}