{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7994GDON",
"aliases": [
"charles-gersbach:hPA-auxiliary-set-perturbseq-10xlane1-CRISPR"
],
"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": "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": "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/"
}
]
},
"award": {
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"component": "functional characterization",
"contact_pi": {
"@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
"title": "Charles Gersbach"
},
"title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6102AFVS/",
"accession": "IGVFDS6102AFVS",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI4132CWBF/",
"accession": "IGVFFI4132CWBF",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in many genes"
}
],
"control_for": [],
"creation_timestamp": "2025-03-28T17:15:47.353778+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/human-donors/IGVFDO6921DDPB/",
"accession": "IGVFDO6921DDPB",
"aliases": [
"charles-gersbach:hPA-donor-34969"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
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"accession": "IGVFFI0515QEWR",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane1-CRISPR-L1-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:11.092564+00:00",
"file_format": "fastq",
"file_size": 1036144769,
"href": "/sequence-files/IGVFFI0515QEWR/@@download/IGVFFI0515QEWR.fastq.gz",
"md5sum": "e26d801296619254ada060e7f55de355",
"s3_uri": "s3://igvf-files/2025/04/09/ac8abbea-a4e0-42f8-9d97-4f36cb3e2061/IGVFFI0515QEWR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_1_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0944TCGC/",
"accession": "IGVFFI0944TCGC",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane1-CRISPR-L1-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:13.398070+00:00",
"file_format": "fastq",
"file_size": 1473771385,
"href": "/sequence-files/IGVFFI0944TCGC/@@download/IGVFFI0944TCGC.fastq.gz",
"md5sum": "5a0e163f13d3daa1883fb1e634ff0aad",
"s3_uri": "s3://igvf-files/2025/04/09/62bb7317-ed1c-4bd5-996e-361fe6e9231d/IGVFFI0944TCGC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_1_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8354OSIZ/",
"accession": "IGVFFI8354OSIZ",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane1-CRISPR-L2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:15.831380+00:00",
"file_format": "fastq",
"file_size": 1020400018,
"href": "/sequence-files/IGVFFI8354OSIZ/@@download/IGVFFI8354OSIZ.fastq.gz",
"md5sum": "f54cab8eee17a246b077317ba0178fe4",
"s3_uri": "s3://igvf-files/2025/04/09/710cbde4-4cbc-46bd-ac3e-c9a50b751006/IGVFFI8354OSIZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_1_S1_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5890JKQC/",
"accession": "IGVFFI5890JKQC",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane1-CRISPR-L2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:18.530258+00:00",
"file_format": "fastq",
"file_size": 1446708199,
"href": "/sequence-files/IGVFFI5890JKQC/@@download/IGVFFI5890JKQC.fastq.gz",
"md5sum": "e3ebc058c22494a61801b83030d272a0",
"s3_uri": "s3://igvf-files/2025/04/09/ef439072-8694-4a6d-b72a-99f349d28c11/IGVFFI5890JKQC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_1_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3025IEAV/",
"accession": "IGVFFI3025IEAV",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane1-CRISPR-L2"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:24.863769+00:00",
"file_format": "yaml",
"file_size": 1445,
"href": "/configuration-files/IGVFFI3025IEAV/@@download/IGVFFI3025IEAV.yaml.gz",
"md5sum": "69de27c3e52bc84154958fb35228b86e",
"s3_uri": "s3://igvf-files/2025/04/09/9320b7b6-3f75-4f75-9887-b667496f78ec/IGVFFI3025IEAV.yaml.gz",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane1-crispr-L2.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8734RNZH/",
"accession": "IGVFFI8734RNZH",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane1-CRISPR-L1"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:21.115026+00:00",
"file_format": "yaml",
"file_size": 1449,
"href": "/configuration-files/IGVFFI8734RNZH/@@download/IGVFFI8734RNZH.yaml.gz",
"md5sum": "43df6f875cfe988eedcc3484c77d1ada",
"s3_uri": "s3://igvf-files/2025/04/09/45a84aeb-2ba6-4355-a2c5-ab32f3d45469/IGVFFI8734RNZH.yaml.gz",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane1-crispr-L1.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0886UBIB/",
"accession": "IGVFDS0886UBIB",
"aliases": [
"charles-gersbach:hPA-measurement-set-perturbseq-10xlane1-GEX"
],
"preferred_assay_title": "Perturb-seq",
"status": "released"
}
],
"release_timestamp": "2025-05-16T16:07:07.728376+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"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/703c3934-6c9b-41d0-8481-e73cc64075f7/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000127/",
"@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": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2025-03-31T14:26:41.345997+00:00",
"summary": "gRNA sequencing for CRISPR activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "b9e74d65-4068-49c7-989f-2059b381093f"
}