{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3872CUHM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3872CUHM",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR1-Rep1_S18",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR2-Rep1_S24",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR3-Rep1_S72",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR4-Rep1_S78"
],
"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 [IGVFDS3872CUHM](/measurement-sets/IGVFDS3872CUHM/) 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/IGVFDS3872CUHM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3872CUHM](/measurement-sets/IGVFDS3872CUHM/) has sequence file(s) [IGVFFI0372HBLG](/sequence-files/IGVFFI0372HBLG/), [IGVFFI5233CFBC](/sequence-files/IGVFFI5233CFBC/), [IGVFFI3691CGEM](/sequence-files/IGVFFI3691CGEM/), [IGVFFI5535XSUG](/sequence-files/IGVFFI5535XSUG/) 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/IGVFDS3872CUHM/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS4597CMXX](/auxiliary-sets/IGVFDS4597CMXX/) 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/IGVFDS4597CMXX/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4941RWXR](/in-vitro-systems/IGVFSM4941RWXR/) 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/IGVFSM4941RWXR/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM4941RWXR](/in-vitro-systems/IGVFSM4941RWXR/) 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/IGVFSM4941RWXR/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4597CMXX/",
"accession": "IGVFDS4597CMXX",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_SSFA2-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/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": "2024-05-14T20:33:17.962777+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/IGVFFI0339WZPU/",
"accession": "IGVFFI0339WZPU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR1-Rep1_S18"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:30.406507+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0339WZPU/@@download/IGVFFI0339WZPU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/95161ab6-72bf-4efa-b0cd-1f09532ea0a4/IGVFFI0339WZPU.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinF-PCR1-Rep1_S18.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4442FACK/",
"accession": "IGVFFI4442FACK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR4-Rep1_S78"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:40.511683+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI4442FACK/@@download/IGVFFI4442FACK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2e00203e-fea5-4b2a-8543-a8b5d7a709bc/IGVFFI4442FACK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinF-PCR4-Rep1_S78.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2892EQYV/",
"accession": "IGVFFI2892EQYV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR3-Rep1_S72"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:24.896036+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2892EQYV/@@download/IGVFFI2892EQYV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a1675eb0-4e5c-42a8-88cf-65e453274e69/IGVFFI2892EQYV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinF-PCR3-Rep1_S72.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2188BZIX/",
"accession": "IGVFFI2188BZIX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR2-Rep1_S24"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:09.202590+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI2188BZIX/@@download/IGVFFI2188BZIX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6051ead9-26a5-4d91-9688-51a2e15aca88/IGVFFI2188BZIX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinF-PCR2-Rep1_S24.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0372HBLG/",
"accession": "IGVFFI0372HBLG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR2-Rep1_S24"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:46:26.115050+00:00",
"file_format": "fastq",
"file_size": 11405375,
"href": "/sequence-files/IGVFFI0372HBLG/@@download/IGVFFI0372HBLG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a0f2b961-dec8-4def-8077-541dfb71d9b1/IGVFFI0372HBLG.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-FF2-BinF-PCR2-Rep1_S24_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5233CFBC/",
"accession": "IGVFFI5233CFBC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR3-Rep1_S72"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:46:43.927293+00:00",
"file_format": "fastq",
"file_size": 20129806,
"href": "/sequence-files/IGVFFI5233CFBC/@@download/IGVFFI5233CFBC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/464f3f73-7625-43c4-93c3-784db2baf3a7/IGVFFI5233CFBC.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-FF2-BinF-PCR3-Rep1_S72_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3691CGEM/",
"accession": "IGVFFI3691CGEM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR4-Rep1_S78"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:02.070989+00:00",
"file_format": "fastq",
"file_size": 20471673,
"href": "/sequence-files/IGVFFI3691CGEM/@@download/IGVFFI3691CGEM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a8d6eafd-54ac-4070-bd6b-6bd225011e6b/IGVFFI3691CGEM.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-FF2-BinF-PCR4-Rep1_S78_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5535XSUG/",
"accession": "IGVFFI5535XSUG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR1-Rep1_S18"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:46:06.874388+00:00",
"file_format": "fastq",
"file_size": 10152043,
"href": "/sequence-files/IGVFFI5535XSUG/@@download/IGVFFI5535XSUG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5abba541-5191-4f3d-a8ac-4f20e5205a09/IGVFFI5535XSUG.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-FF2-BinF-PCR1-Rep1_S18_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": "2024-07-10T19:51:58.237598+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4941RWXR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4941RWXR",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR1-Rep1_S18",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR2-Rep1_S24",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR3-Rep1_S72",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinF-PCR4-Rep1_S78"
],
"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": "2024-06-01T01:46:06.874388+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": "4f3c25a4-d19c-42e9-b05d-af476179035d"
}