{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9457SBWA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9457SBWA",
"aliases": [
"guillaume-lettre:BP_screen_ABE8_R_R4_2_ms"
],
"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": "mismatched status",
"detail": "Released in vitro system [IGVFSM6979SEVH](/in-vitro-systems/IGVFSM6979SEVH/) has in progress subobject construct library set [IGVFDS7830RLQN](/construct-library-sets/IGVFDS7830RLQN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6979SEVH/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6979SEVH](/in-vitro-systems/IGVFSM6979SEVH/) has in progress subobject crispr modification [53d408bd-fa43-4ed3-be6d-db4ab82f7820](/crispr-modifications/53d408bd-fa43-4ed3-be6d-db4ab82f7820/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6979SEVH/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6979SEVH](/in-vitro-systems/IGVFSM6979SEVH/) has in progress subobject construct library set [IGVFDS0313HDTK](/construct-library-sets/IGVFDS0313HDTK/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6979SEVH/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6979SEVH](/in-vitro-systems/IGVFSM6979SEVH/) 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/IGVFSM6979SEVH/"
},
{
"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": "missing publication",
"detail": "Measurement set [IGVFDS9457SBWA](/measurement-sets/IGVFDS9457SBWA/) 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/IGVFDS9457SBWA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9457SBWA](/measurement-sets/IGVFDS9457SBWA/) has sequence file(s): [IGVFFI6013BAKU](/sequence-files/IGVFFI6013BAKU/), [IGVFFI5859LZRA](/sequence-files/IGVFFI5859LZRA/) 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/IGVFDS9457SBWA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9457SBWA](/measurement-sets/IGVFDS9457SBWA/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS9457SBWA/"
}
]
},
"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/IGVFDS7830RLQN/",
"accession": "IGVFDS7830RLQN",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI6052MTJM/",
"accession": "IGVFFI6052MTJM",
"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"
},
{
"@id": "/construct-library-sets/IGVFDS0313HDTK/",
"accession": "IGVFDS0313HDTK",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI6052MTJM/",
"accession": "IGVFFI6052MTJM",
"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": "2024-11-15T20:01:18.506892+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/IGVFFI6013BAKU/",
"accession": "IGVFFI6013BAKU",
"aliases": [
"guillaume-lettre:BP_screen_ABE8_R_R4_2_read2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T20:46:21.117790+00:00",
"file_format": "fastq",
"file_size": 974082807,
"href": "/sequence-files/IGVFFI6013BAKU/@@download/IGVFFI6013BAKU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/1b20b459-9353-47c6-ae4f-901d8dae0767/IGVFFI6013BAKU.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/BE_IGVF_20230720/samples/NS.X0070.001.IndexR1_51.R_R4_2_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5859LZRA/",
"accession": "IGVFFI5859LZRA",
"aliases": [
"guillaume-lettre:BP_screen_ABE8_R_R4_2_read1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T20:22:39.325596+00:00",
"file_format": "fastq",
"file_size": 796736927,
"href": "/sequence-files/IGVFFI5859LZRA/@@download/IGVFFI5859LZRA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/69444fcb-e051-408f-be0c-dafae3b4c6ee/IGVFFI5859LZRA.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/BE_IGVF_20230720/samples/NS.X0070.001.IndexR1_51.R_R4_2_R1.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4607KRIY/"
],
"lab": {
"@id": "/labs/guillaume-lettre/",
"title": "Guillaume Lettre, MHI"
},
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/adenine-base-editing-abe-screening-of-blood-pressu-261geroqwl47/v1"
],
"release_timestamp": "2025-03-07T22:26:15.161098+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6979SEVH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6979SEVH",
"aliases": [
"guillaume-lettre:BP_screen_ABE8_R_R4_2_ivs"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/53d408bd-fa43-4ed3-be6d-db4ab82f7820/",
"modality": "base editing",
"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 (sorting details: FACS 60-80% expression of NFKBIA) modified with CRISPR base editing SpRY-ABE8e, 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": "2024-11-15T20:22:39.325596+00:00",
"summary": "CRISPR base editing FlowFISH screen sorted on the expression of NFKBIA integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide associated with blood pressure",
"targeted_genes": [
{
"@id": "/genes/ENSG00000100906/",
"geneid": "ENSG00000100906",
"name": "NFKB inhibitor alpha",
"status": "released",
"symbol": "NFKBIA",
"synonyms": [
"NFKB inhibitor alpha",
"EDAID2",
"nuclear factor of kappa light chain gene enhancer in B-cells",
"nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha",
"IkappaBalpha",
"major histocompatibility complex enhancer-binding protein MAD3",
"ikB-alpha",
"NF-kappa-B inhibitor alpha",
"I-kappa-B-alpha",
"MAD-3",
"IKBA",
"NFKBIA",
"NFKBI"
]
}
],
"uuid": "f97a277b-df2e-4f06-9f3b-93ace13f9436"
}