{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2496GSOR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2496GSOR",
"aliases": [
"daniel-bauer:ChrX_Screen_no_deaminase_day7_rep2_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": "mismatched status",
"detail": "Released in vitro system [IGVFSM5589ZXUY](/in-vitro-systems/IGVFSM5589ZXUY/) has in progress subobject construct library set [IGVFDS7616NEZY](/construct-library-sets/IGVFDS7616NEZY/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM5589ZXUY/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5589ZXUY](/in-vitro-systems/IGVFSM5589ZXUY/) has in progress subobject crispr modification [f1d5cc0b-e434-4c94-ae60-1469a0af0ef8](/crispr-modifications/f1d5cc0b-e434-4c94-ae60-1469a0af0ef8/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM5589ZXUY/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2496GSOR](/measurement-sets/IGVFDS2496GSOR/) has sequence file(s): [IGVFFI9574IFKA](/sequence-files/IGVFFI9574IFKA/), [IGVFFI7284WKRD](/sequence-files/IGVFFI7284WKRD/) 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/IGVFDS2496GSOR/"
}
]
},
"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/IGVFDS7616NEZY/",
"accession": "IGVFDS7616NEZY",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI1727UGRE/",
"accession": "IGVFFI1727UGRE",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "GRCh38 guide RNA sequences"
},
{
"@id": "/tabular-files/IGVFFI7806CLOH/",
"accession": "IGVFFI7806CLOH",
"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": "2024-09-10T17:28:59.293081+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0965QSBA/",
"accession": "IGVFDO0965QSBA",
"aliases": [
"igvf:donor_of_HUDEP-2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9574IFKA/",
"accession": "IGVFFI9574IFKA",
"aliases": [
"daniel-bauer:ChrX_Screen_no_deaminase_day7_rep2_read1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-09-10T17:30:44.306564+00:00",
"file_format": "fastq",
"file_size": 212525761,
"href": "/sequence-files/IGVFFI9574IFKA/@@download/IGVFFI9574IFKA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/09/10/5a44bdd8-4bec-4160-ad6a-e4b510698866/IGVFFI9574IFKA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/data/pinello/PROJECTS/2024_02_EC_ChrX/submitted_files/ChrX_Screen_#AACCGat_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7284WKRD/",
"accession": "IGVFFI7284WKRD",
"aliases": [
"daniel-bauer:ChrX_Screen_no_deaminase_day7_rep2_read2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-09-10T17:35:39.118368+00:00",
"file_format": "fastq",
"file_size": 222979029,
"href": "/sequence-files/IGVFFI7284WKRD/@@download/IGVFFI7284WKRD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/09/10/1e42eb54-a25e-4eeb-853d-9817cb96d672/IGVFFI7284WKRD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/data/pinello/PROJECTS/2024_02_EC_ChrX/submitted_files/ChrX_Screen_#AACCGat_R2.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0120EBCZ/"
],
"lab": {
"@id": "/labs/daniel-bauer/",
"title": "Daniel Bauer, HSCI"
},
"preferred_assay_title": "Proliferation CRISPR screen",
"protocols": [
"https://www.protocols.io/view/chrx-variant-installation-protocol-5jyl8dmndg2w/v1"
],
"release_timestamp": "2025-03-07T22:24:56.703058+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5589ZXUY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5589ZXUY",
"aliases": [
"daniel-bauer:ChrX_Screen_no_deaminase_day7_rep2_ivs"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/f1d5cc0b-e434-4c94-ae60-1469a0af0ef8/",
"modality": "cutting",
"status": "in progress"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0022838/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HUDEP-2"
],
"status": "released",
"summary": "HUDEP-2",
"term_name": "HUDEP-2"
}
],
"status": "released",
"summary": "HUDEP-2 cell line, Homo sapiens modified with CRISPR cutting SpRY, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "25",
"status": "released",
"submitted_by": {
"@id": "/users/96fd4846-bfa6-47db-ac12-495df29943ee/",
"title": "Eric Che"
},
"submitted_files_timestamp": "2024-09-10T17:30:44.306564+00:00",
"summary": "Proliferation CRISPR cutting screen integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide",
"uuid": "f0252b9d-6d18-4253-b709-b3e7c4296eb7"
}