{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0886UBIB",
"aliases": [
"charles-gersbach:hPA-measurement-set-perturbseq-10xlane1-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": "mismatched status",
"detail": "Released primary cell [IGVFSM7138HWZK](/primary-cells/IGVFSM7138HWZK/) 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/IGVFSM7138HWZK/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM7138HWZK](/primary-cells/IGVFSM7138HWZK/) 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/IGVFSM7138HWZK/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM7138HWZK](/primary-cells/IGVFSM7138HWZK/) 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/IGVFSM7138HWZK/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0886UBIB](/measurement-sets/IGVFDS0886UBIB/) 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/IGVFDS0886UBIB/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS7994GDON](/auxiliary-sets/IGVFDS7994GDON/) 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/IGVFDS7994GDON/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7138HWZK](/primary-cells/IGVFSM7138HWZK/) 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/IGVFSM7138HWZK/"
},
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS0886UBIB](/measurement-sets/IGVFDS0886UBIB/) 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/IGVFDS0886UBIB/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7994GDON](/auxiliary-sets/IGVFDS7994GDON/) 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/IGVFDS7994GDON/"
}
]
},
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{
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"aliases": [
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],
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"status": "released"
}
],
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"title": "Charles Gersbach"
},
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},
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{
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{
"@id": "/tabular-files/IGVFFI4132CWBF/",
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"summary": "guide RNA sequences"
}
],
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}
],
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"creation_timestamp": "2025-03-28T17:18:27.788894+00:00",
"data_use_limitation_summaries": [
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],
"donors": [
{
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"aliases": [
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],
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}
],
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"file_set_type": "experimental data",
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"aliases": [
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],
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"creation_timestamp": "2025-04-09T21:03:46.787126+00:00",
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"href": "/sequence-files/IGVFFI6836LINK/@@download/IGVFFI6836LINK.fastq.gz",
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},
{
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"accession": "IGVFFI8843ZBZD",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane1-GEX-L1-R1"
],
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"creation_timestamp": "2025-04-09T21:03:40.473391+00:00",
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"href": "/sequence-files/IGVFFI8843ZBZD/@@download/IGVFFI8843ZBZD.fastq.gz",
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},
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"submitted_file_name": "/work/rr151/SamAIM2neuro_data/GEX_1_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9089DYXF/",
"accession": "IGVFFI9089DYXF",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane1-GEX-L1-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:03:44.417385+00:00",
"file_format": "fastq",
"file_size": 8346127235,
"href": "/sequence-files/IGVFFI9089DYXF/@@download/IGVFFI9089DYXF.fastq.gz",
"md5sum": "4b63615c8d3e6f8dc5bb57144151b3ef",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
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"submitted_file_name": "/work/rr151/SamAIM2neuro_data/GEX_1_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8214WEZU/",
"accession": "IGVFFI8214WEZU",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane1-GEX-L2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:03:49.849167+00:00",
"file_format": "fastq",
"file_size": 8288656783,
"href": "/sequence-files/IGVFFI8214WEZU/@@download/IGVFFI8214WEZU.fastq.gz",
"md5sum": "1a7c943c22bb38e4682808e3c617d075",
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"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/GEX_1_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6587ONPF/",
"accession": "IGVFFI6587ONPF",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane1-GEX-L1"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:05.244720+00:00",
"file_format": "yaml",
"file_size": 1304,
"href": "/configuration-files/IGVFFI6587ONPF/@@download/IGVFFI6587ONPF.yaml.gz",
"md5sum": "6407a9917f57ea9247b8c9658795274d",
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"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane1-GEX-L1.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5434WWKW/",
"accession": "IGVFFI5434WWKW",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane1-GEX-L2"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:08.362778+00:00",
"file_format": "yaml",
"file_size": 1306,
"href": "/configuration-files/IGVFFI5434WWKW/@@download/IGVFFI5434WWKW.yaml.gz",
"md5sum": "c2a2eb797fe31034228deca2ff328be3",
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"status": "released",
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"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": "2025-05-16T16:07:07.546802+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM7138HWZK/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7138HWZK",
"aliases": [
"charles-gersbach:hPA-primary-cell-perturbseq-10xlane1"
],
"classifications": [
"primary cell"
],
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"modifications": [
{
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"modality": "activation",
"status": "released"
}
],
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{
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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": "2025-03-28T19:07:56.657602+00:00",
"summary": "CRISPR activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "68c2ef9e-528d-4379-ac5c-dcdc8835d335"
}