{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7222TNKJ",
"aliases": [
"guillaume-lettre:BP_screen_KRAB_PROLIF_R2_2_ms"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003659/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7222TNKJ](/measurement-sets/IGVFDS7222TNKJ/) 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/IGVFDS7222TNKJ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7222TNKJ](/measurement-sets/IGVFDS7222TNKJ/) has sequence file(s): [IGVFFI8190YGNW](/sequence-files/IGVFFI8190YGNW/), [IGVFFI6163GMVE](/sequence-files/IGVFFI6163GMVE/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS7222TNKJ/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000753/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6947JXBN](/in-vitro-systems/IGVFSM6947JXBN/) has in progress subobject crispr modification [dca41650-4b6d-4685-b9c0-6c003f2d872a](/crispr-modifications/dca41650-4b6d-4685-b9c0-6c003f2d872a/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6947JXBN/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6947JXBN](/in-vitro-systems/IGVFSM6947JXBN/) has in progress subobject construct library set [IGVFDS3175SLZT](/construct-library-sets/IGVFDS3175SLZT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6947JXBN/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6947JXBN](/in-vitro-systems/IGVFSM6947JXBN/) has in progress subobject construct library set [IGVFDS2633QETV](/construct-library-sets/IGVFDS2633QETV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6947JXBN/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6947JXBN](/in-vitro-systems/IGVFSM6947JXBN/) 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/IGVFSM6947JXBN/"
}
]
},
"award": {
"@id": "/awards/HG012010/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/3439b15d-c35b-4991-a77d-8feb104d3642/",
"title": "Luca Pinello"
},
"title": "Comprehensive characterization of variants underlying heart and blood diseases with CRISPR base editing"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2633QETV/",
"accession": "IGVFDS2633QETV",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI3496FQXK/",
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"summary": "GRCh38 guide RNA sequences"
},
{
"@id": "/tabular-files/IGVFFI0132XPDE/",
"accession": "IGVFFI0132XPDE",
"content_type": "variants",
"status": "in progress",
"summary": "GRCh38 variants"
}
],
"status": "in progress",
"summary": "guide (sgRNA) library targeting phenotype-associated variants genome-wide associated with blood pressure"
},
{
"@id": "/construct-library-sets/IGVFDS3175SLZT/",
"accession": "IGVFDS3175SLZT",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI3496FQXK/",
"accession": "IGVFFI3496FQXK",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "GRCh38 guide RNA sequences"
},
{
"@id": "/tabular-files/IGVFFI0132XPDE/",
"accession": "IGVFFI0132XPDE",
"content_type": "variants",
"status": "in progress",
"summary": "GRCh38 variants"
}
],
"status": "in progress",
"summary": "guide (sgRNA) library targeting phenotype-associated variants genome-wide associated with blood pressure"
}
],
"control_for": [],
"creation_timestamp": "2024-11-15T20:01:32.506683+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI8190YGNW/",
"accession": "IGVFFI8190YGNW",
"aliases": [
"guillaume-lettre:BP_screen_KRAB_PROLIF_R2_2_read1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T20:52:31.890569+00:00",
"file_format": "fastq",
"file_size": 961617667,
"href": "/sequence-files/IGVFFI8190YGNW/@@download/IGVFFI8190YGNW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/1b4f8475-4568-4b9b-bac8-a8f13af94f99/IGVFFI8190YGNW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/home/lokensin/projects/rrg-glettre/sequencing_datastore/raw_data/CRISPR_IGVF_20230720/samples/NS.X0085.005.IndexR1_06.P2BPR2_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6163GMVE/",
"accession": "IGVFFI6163GMVE",
"aliases": [
"guillaume-lettre:BP_screen_KRAB_PROLIF_R2_2_read2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T21:15:15.192415+00:00",
"file_format": "fastq",
"file_size": 1391723894,
"href": "/sequence-files/IGVFFI6163GMVE/@@download/IGVFFI6163GMVE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/37460cff-4463-4b78-94da-bfc5e97f539b/IGVFFI6163GMVE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/home/lokensin/projects/rrg-glettre/sequencing_datastore/raw_data/CRISPR_IGVF_20230720/samples/NS.X0085.005.IndexR1_06.P2BPR2_R2.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0577SVCR/"
],
"lab": {
"@id": "/labs/guillaume-lettre/",
"title": "Guillaume Lettre, MHI"
},
"preferred_assay_title": "Proliferation CRISPR screen",
"protocols": [
"https://www.protocols.io/view/crispri-screening-for-functional-characterization-5qpvo9ybxv4o/v1"
],
"release_timestamp": "2025-03-07T22:27:42.240002+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6947JXBN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6947JXBN",
"aliases": [
"guillaume-lettre:BP_screen_KRAB_PROLIF_R2_2_ivs"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/dca41650-4b6d-4685-b9c0-6c003f2d872a/",
"modality": "interference",
"status": "in progress"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "Homo sapiens (female) TeloHAEC cell line modified with CRISPRi Sp-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/005a9a1c-02ab-408f-90a9-d6bea5c36d05/",
"title": "Ken Sin Lo"
},
"submitted_files_timestamp": "2024-11-15T20:52:31.890569+00:00",
"summary": "Proliferation CRISPR interference screen integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide associated with blood pressure",
"uuid": "899f64c4-1ea7-4951-a466-4544105a96df"
}