{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4521RIQF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4521RIQF",
"aliases": [
"charles-gersbach:hPA-measurement-set-perturbseq-10xlane4-GEX"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"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/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4521RIQF](/measurement-sets/IGVFDS4521RIQF/) 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/IGVFDS4521RIQF/"
}
],
"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/"
},
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS4521RIQF](/measurement-sets/IGVFDS4521RIQF/) 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": "/measurement-sets/IGVFDS4521RIQF/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7160FCCA/",
"accession": "IGVFDS7160FCCA",
"aliases": [
"charles-gersbach:hPA-auxiliary-set-perturbseq-10xlane4-CRISPR"
],
"file_set_type": "gRNA sequencing",
"status": "released"
}
],
"award": {
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"component": "functional characterization",
"contact_pi": {
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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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"file_set_type": "guide library",
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{
"@id": "/tabular-files/IGVFFI4132CWBF/",
"accession": "IGVFFI4132CWBF",
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"status": "released",
"summary": "guide RNA sequences"
}
],
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"summary": "guide (sgRNA) library targeting transcription start sites in many genes"
}
],
"control_for": [],
"creation_timestamp": "2025-03-28T17:18:31.397781+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
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"accession": "IGVFDO6216GVYW",
"aliases": [
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],
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"status": "released",
"taxa": "Homo sapiens"
}
],
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"file_set_type": "experimental data",
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{
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"accession": "IGVFFI8171XOZL",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane4-GEX-L1-R1"
],
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"controlled_access": false,
"creation_timestamp": "2025-04-09T21:03:59.250777+00:00",
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"file_size": 3794822633,
"href": "/sequence-files/IGVFFI8171XOZL/@@download/IGVFFI8171XOZL.fastq.gz",
"md5sum": "88d4a45c610ed8338e98a832a0f03767",
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"term_name": "Illumina NovaSeq 6000"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0949WBOD/",
"accession": "IGVFFI0949WBOD",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane4-GEX-L1-R2"
],
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"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:01.830167+00:00",
"file_format": "fastq",
"file_size": 9317499913,
"href": "/sequence-files/IGVFFI0949WBOD/@@download/IGVFFI0949WBOD.fastq.gz",
"md5sum": "c73a5cc003c038b52f16416761cfc6ab",
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"term_name": "Illumina NovaSeq 6000"
},
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"submitted_file_name": "/work/rr151/SamAIM2neuro_data/GEX_4_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7195IFIQ/",
"accession": "IGVFFI7195IFIQ",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane4-GEX-L2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:05.368617+00:00",
"file_format": "fastq",
"file_size": 3779829863,
"href": "/sequence-files/IGVFFI7195IFIQ/@@download/IGVFFI7195IFIQ.fastq.gz",
"md5sum": "0561469b0ad055bf6c3a9a591b1ebed6",
"s3_uri": "s3://igvf-files/2025/04/09/5d70b09d-b14c-424a-a3a5-a2bb089367ba/IGVFFI7195IFIQ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/GEX_4_S4_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3023HOII/",
"accession": "IGVFFI3023HOII",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane4-GEX-L2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:08.146597+00:00",
"file_format": "fastq",
"file_size": 9263790502,
"href": "/sequence-files/IGVFFI3023HOII/@@download/IGVFFI3023HOII.fastq.gz",
"md5sum": "c02eced43c21f2cde40d6ace9bb1e2d1",
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/GEX_4_S4_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2259SIES/",
"accession": "IGVFFI2259SIES",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane4-GEX-L1"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:16.362556+00:00",
"file_format": "yaml",
"file_size": 1304,
"href": "/configuration-files/IGVFFI2259SIES/@@download/IGVFFI2259SIES.yaml.gz",
"md5sum": "a0480737c9ca8d79a82913f45ef3fdc8",
"s3_uri": "s3://igvf-files/2025/04/09/110ef152-b27a-45af-ac4e-3e736e7bf4de/IGVFFI2259SIES.yaml.gz",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane4-GEX-L1.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4747OOCN/",
"accession": "IGVFFI4747OOCN",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane4-GEX-L2"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:18.839369+00:00",
"file_format": "yaml",
"file_size": 1303,
"href": "/configuration-files/IGVFFI4747OOCN/@@download/IGVFFI4747OOCN.yaml.gz",
"md5sum": "a8bfcbb87e5e995cf46f69284ebd2d67",
"s3_uri": "s3://igvf-files/2025/04/09/ea24cb28-7bdf-4df0-ad00-754844d41a16/IGVFFI4747OOCN.yaml.gz",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane4-GEX-L2.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"notes": "This measurement set previously used 5' to 3' as strand_specificity, but the strand_specificity has now been updated to 5 prime to 3 prime via an upgrade.",
"onlist_files": [
"/tabular-files/IGVFFI9487JPEN/"
],
"onlist_method": "no combination",
"preferred_assay_title": "Perturb-seq",
"protocols": [
"https://www.protocols.io/view/human-primary-astrocyte-hpa-culture-x54v97jwzg3e/v1",
"https://www.protocols.io/view/human-primary-astrocyte-hpa-crispra-reprogramming-ewov12477gr2/v1"
],
"release_timestamp": "2025-05-16T16:07:12.840271+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": [
{
"@id": "/crispr-modifications/703c3934-6c9b-41d0-8481-e73cc64075f7/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
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"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "astrocyte",
"term_name": "astrocyte"
}
],
"status": "released",
"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": [
{
"@id": "/treatments/c7e73583-b639-473f-84c4-947cdc0bd81d/",
"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": "29",
"status": "released",
"strand_specificity": "5 prime to 3 prime",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2025-03-28T19:08:10.445845+00:00",
"summary": "CRISPR activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "3808bcce-cbe9-4613-896c-59aa00ae308e"
}