{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7160FCCA",
"aliases": [
"charles-gersbach:hPA-auxiliary-set-perturbseq-10xlane4-CRISPR"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS7160FCCA](/auxiliary-sets/IGVFDS7160FCCA/) 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/IGVFDS7160FCCA/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM2166MHKA](/primary-cells/IGVFSM2166MHKA/) has in progress subobject treatment [c7e73583-b639-473f-84c4-947cdc0bd81d](/treatments/c7e73583-b639-473f-84c4-947cdc0bd81d/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM2166MHKA/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM2166MHKA](/primary-cells/IGVFSM2166MHKA/) has in progress subobject treatment [e23aab02-ae82-4935-85ad-1f238757f3ba](/treatments/e23aab02-ae82-4935-85ad-1f238757f3ba/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM2166MHKA/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM2166MHKA](/primary-cells/IGVFSM2166MHKA/) 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": "/primary-cells/IGVFSM2166MHKA/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7160FCCA](/auxiliary-sets/IGVFDS7160FCCA/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/auxiliary-sets/IGVFDS7160FCCA/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2166MHKA](/primary-cells/IGVFSM2166MHKA/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM2166MHKA/"
}
]
},
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"title": "Charles Gersbach"
},
"title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
},
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{
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{
"@id": "/tabular-files/IGVFFI4132CWBF/",
"accession": "IGVFFI4132CWBF",
"content_type": "guide RNA sequences",
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}
],
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}
],
"control_for": [],
"creation_timestamp": "2025-03-28T17:15:50.195314+00:00",
"data_use_limitation_summaries": [
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],
"donors": [
{
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"aliases": [
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],
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"taxa": "Homo sapiens"
}
],
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"files": [
{
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"accession": "IGVFFI5902VIRS",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:31.289418+00:00",
"file_format": "fastq",
"file_size": 945481334,
"href": "/sequence-files/IGVFFI5902VIRS/@@download/IGVFFI5902VIRS.fastq.gz",
"md5sum": "890e31d3f31f5c71a884bd494e1a3015",
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},
{
"@id": "/sequence-files/IGVFFI2728ZPGG/",
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],
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"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:34.091651+00:00",
"file_format": "fastq",
"file_size": 1369440043,
"href": "/sequence-files/IGVFFI2728ZPGG/@@download/IGVFFI2728ZPGG.fastq.gz",
"md5sum": "3b80c84cba4e6716f1b642b1a0879c6d",
"s3_uri": "s3://igvf-files/2025/04/09/9b46905b-4297-4dd9-a4a6-d6cf9ff905b4/IGVFFI2728ZPGG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_4_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1449FMDD/",
"accession": "IGVFFI1449FMDD",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane4-CRISPR-L2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:36.623973+00:00",
"file_format": "fastq",
"file_size": 928810199,
"href": "/sequence-files/IGVFFI1449FMDD/@@download/IGVFFI1449FMDD.fastq.gz",
"md5sum": "08d6d207057cd8bbe35892ad944a6374",
"s3_uri": "s3://igvf-files/2025/04/09/b6175d59-23ae-4ed9-ac37-2e7b10f01a73/IGVFFI1449FMDD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_4_S4_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2664QRZC/",
"accession": "IGVFFI2664QRZC",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane4-CRISPR-L2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:39.469522+00:00",
"file_format": "fastq",
"file_size": 1340959267,
"href": "/sequence-files/IGVFFI2664QRZC/@@download/IGVFFI2664QRZC.fastq.gz",
"md5sum": "0effb6289b4a7ec63da13ca5f11af7b6",
"s3_uri": "s3://igvf-files/2025/04/09/fe45b1ae-7b8b-427f-915d-b8a6355b237e/IGVFFI2664QRZC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_4_S4_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1763IVWB/",
"accession": "IGVFFI1763IVWB",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane4-CRISPR-L1"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:33.329760+00:00",
"file_format": "yaml",
"file_size": 1445,
"href": "/configuration-files/IGVFFI1763IVWB/@@download/IGVFFI1763IVWB.yaml.gz",
"md5sum": "211fd8d1f3269da5f0ae6659e4b7c715",
"s3_uri": "s3://igvf-files/2025/04/09/d66b8c42-73e3-45c7-a121-5abd20d6a316/IGVFFI1763IVWB.yaml.gz",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane4-crispr-L1.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3935RVGM/",
"accession": "IGVFFI3935RVGM",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane4-CRISPR-L2"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:35.409949+00:00",
"file_format": "yaml",
"file_size": 1441,
"href": "/configuration-files/IGVFFI3935RVGM/@@download/IGVFFI3935RVGM.yaml.gz",
"md5sum": "933b303266f1f0fe7ce2090628004af7",
"s3_uri": "s3://igvf-files/2025/04/09/60e73d9b-0211-48d5-ad5c-0e87615a6943/IGVFFI3935RVGM.yaml.gz",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane4-crispr-L2.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4521RIQF/",
"accession": "IGVFDS4521RIQF",
"aliases": [
"charles-gersbach:hPA-measurement-set-perturbseq-10xlane4-GEX"
],
"preferred_assay_title": "Perturb-seq",
"status": "released"
}
],
"release_timestamp": "2025-05-16T16:07:12.878292+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM2166MHKA/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2166MHKA",
"aliases": [
"charles-gersbach:hPA-primary-cell-perturbseq-10xlane4"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
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"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000127/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "astrocyte",
"term_name": "astrocyte"
}
],
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"summary": "Homo sapiens astrocyte cell treated with 10 ng/mL Neurotrophin-3, 20 ng/mL Brain-Derived Neurotrophic Factor, modified with CRISPRa Sp-dCas9-2xVP64-2A-Puro, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
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"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 20 ng/mL Brain-Derived Neurotrophic Factor",
"treatment_term_name": "Brain-Derived Neurotrophic Factor",
"treatment_type": "protein"
},
{
"@id": "/treatments/e23aab02-ae82-4935-85ad-1f238757f3ba/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 10 ng/mL Neurotrophin-3",
"treatment_term_name": "Neurotrophin-3",
"treatment_type": "protein"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2025-03-31T14:26:56.657638+00:00",
"summary": "gRNA sequencing for CRISPR activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "de98242b-7aa1-45c9-a860-5e4d9d353c6a"
}