{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7237TBXX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7237TBXX",
"aliases": [
"richard-sherwood:18loci_uptake_Rep3_bottom40_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 sequence file [IGVFFI8933KBNG](/sequence-files/IGVFFI8933KBNG/) has in progress subobject platform term [NTR_0000785](/platform-terms/NTR_0000785/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/sequence-files/IGVFFI8933KBNG/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1124PLAC](/in-vitro-systems/IGVFSM1124PLAC/) has in progress subobject construct library set [IGVFDS5242VHWM](/construct-library-sets/IGVFDS5242VHWM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM1124PLAC/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1124PLAC](/in-vitro-systems/IGVFSM1124PLAC/) has in progress subobject crispr modification [464b468a-3a69-4880-96b1-3a5efa246118](/crispr-modifications/464b468a-3a69-4880-96b1-3a5efa246118/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM1124PLAC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7237TBXX](/measurement-sets/IGVFDS7237TBXX/) has sequence file(s) [IGVFFI7249TTXU](/sequence-files/IGVFFI7249TTXU/), [IGVFFI8933KBNG](/sequence-files/IGVFFI8933KBNG/) 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/IGVFDS7237TBXX/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7237TBXX](/measurement-sets/IGVFDS7237TBXX/) has sequence file(s): [IGVFFI7249TTXU](/sequence-files/IGVFFI7249TTXU/), [IGVFFI8933KBNG](/sequence-files/IGVFFI8933KBNG/) 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/IGVFDS7237TBXX/"
},
{
"category": "mismatched status",
"detail": "Released sequence file [IGVFFI7249TTXU](/sequence-files/IGVFFI7249TTXU/) has in progress subobject platform term [NTR_0000785](/platform-terms/NTR_0000785/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/sequence-files/IGVFFI7249TTXU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7237TBXX](/measurement-sets/IGVFDS7237TBXX/) 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/IGVFDS7237TBXX/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS7237TBXX](/measurement-sets/IGVFDS7237TBXX/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 40,
"level_name": "WARNING",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS7237TBXX/"
}
]
},
"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/IGVFDS5242VHWM/",
"accession": "IGVFDS5242VHWM",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI4591THXG/",
"accession": "IGVFFI4591THXG",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "GRCh38 guide RNA sequences"
},
{
"@id": "/tabular-files/IGVFFI6659OUII/",
"accession": "IGVFFI6659OUII",
"content_type": "variants",
"status": "in progress",
"summary": "GRCh38 variants"
}
],
"status": "in progress",
"summary": "guide (sgRNA) library targeting phenotype-associated variants genome-wide"
}
],
"control_for": [],
"creation_timestamp": "2024-11-20T19:58:08.723250+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2837BRET/",
"accession": "IGVFDO2837BRET",
"aliases": [
"igvf:donor_of_HepG2"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7249TTXU/",
"accession": "IGVFFI7249TTXU",
"aliases": [
"richard-sherwood:18loci_uptake_Rep3_bottom40_read1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-20T20:00:51.527127+00:00",
"file_format": "fastq",
"file_size": 11482926,
"href": "/sequence-files/IGVFFI7249TTXU/@@download/IGVFFI7249TTXU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/20/9e776016-fb04-428c-92ac-2b9eb9155625/IGVFFI7249TTXU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/NTR_0000785/",
"status": "in progress",
"term_name": "Element Biosciences AVITI"
},
"status": "released",
"submitted_file_name": "/net/bgm/sherwood/Tian_demult_data/nextseq_051523_Tian/fixed/18loci_uptake_Rep3_bottom40_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8933KBNG/",
"accession": "IGVFFI8933KBNG",
"aliases": [
"richard-sherwood:18loci_uptake_Rep3_bottom40_read2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-20T20:05:18.941120+00:00",
"file_format": "fastq",
"file_size": 15324807,
"href": "/sequence-files/IGVFFI8933KBNG/@@download/IGVFFI8933KBNG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/20/bfe342da-1ab0-49e3-805b-246a68293cfa/IGVFFI8933KBNG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/NTR_0000785/",
"status": "in progress",
"term_name": "Element Biosciences AVITI"
},
"status": "released",
"submitted_file_name": "/net/bgm/sherwood/Tian_demult_data/nextseq_051523_Tian/fixed/18loci_uptake_Rep3_bottom40_R2.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0021NCLH/"
],
"lab": {
"@id": "/labs/richard-sherwood/",
"title": "Richard Sherwood, Brigham and Women's Hospital"
},
"preferred_assay_title": "CRISPR FACS screen",
"protocols": [
"https://www.protocols.io/view/18-loci-variant-installation-protocol-abe-ldluptak-eq2ly638egx9/v1"
],
"release_timestamp": "2025-03-07T22:25:23.105661+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1124PLAC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1124PLAC",
"aliases": [
"richard-sherwood:18loci_uptake_Rep3_bottom40_ivs"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/464b468a-3a69-4880-96b1-3a5efa246118/",
"modality": "base editing",
"status": "in progress"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001187/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HepG2"
],
"status": "released",
"summary": "HepG2",
"term_name": "HepG2"
}
],
"status": "released",
"summary": "HepG2 cell line, male, Homo sapiens (sorting details: Sorted for Bottom 20-40% LDL-C uptake) modified with CRISPR base editing SpRY-ABE8e, transduced (lentivirus) with a guide library (MOI of 0.5)",
"taxa": "Homo sapiens"
}
],
"schema_version": "25",
"status": "released",
"submitted_by": {
"@id": "/users/892d6eba-c6de-4b35-89ff-639c5c5390c9/",
"title": "Quang Vinh Phan"
},
"submitted_files_timestamp": "2024-11-20T20:00:51.527127+00:00",
"summary": "CRISPR base editing FACS screen integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide",
"uuid": "42dee151-0f10-43be-8d5c-2dd7e3dc41b7"
}