{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1645YFQD/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1645YFQD",
"aliases": [
"charles-gersbach:hPA-auxiliary-set-perturbseq-10xlane2-CRISPR"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM6449HHZS](/primary-cells/IGVFSM6449HHZS/) 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/IGVFSM6449HHZS/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM6449HHZS](/primary-cells/IGVFSM6449HHZS/) 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/IGVFSM6449HHZS/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM6449HHZS](/primary-cells/IGVFSM6449HHZS/) 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/IGVFSM6449HHZS/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS1645YFQD](/auxiliary-sets/IGVFDS1645YFQD/) 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/IGVFDS1645YFQD/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6449HHZS](/primary-cells/IGVFSM6449HHZS/) 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/IGVFSM6449HHZS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1645YFQD](/auxiliary-sets/IGVFDS1645YFQD/) 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/IGVFDS1645YFQD/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"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": "2025-03-28T17:15:48.929413+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": [
{
"@id": "/sequence-files/IGVFFI3480QVKK/",
"accession": "IGVFFI3480QVKK",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane2-CRISPR-L2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:29.280948+00:00",
"file_format": "fastq",
"file_size": 1643715692,
"href": "/sequence-files/IGVFFI3480QVKK/@@download/IGVFFI3480QVKK.fastq.gz",
"md5sum": "135be8a3fc190f380de1540089535812",
"s3_uri": "s3://igvf-files/2025/04/09/525c3e57-3150-4177-8e25-bf32cadc8b5d/IGVFFI3480QVKK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_2_S2_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3230TOXA/",
"accession": "IGVFFI3230TOXA",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane2-CRISPR-L1-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:21.005661+00:00",
"file_format": "fastq",
"file_size": 1131938033,
"href": "/sequence-files/IGVFFI3230TOXA/@@download/IGVFFI3230TOXA.fastq.gz",
"md5sum": "281e196b67843cdf36a7f82fe2de8db7",
"s3_uri": "s3://igvf-files/2025/04/09/cd65a327-3f8e-4aa8-8c80-a87a2ad0f66e/IGVFFI3230TOXA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_2_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4242BBXO/",
"accession": "IGVFFI4242BBXO",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane2-CRISPR-L1-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:24.057288+00:00",
"file_format": "fastq",
"file_size": 1678799118,
"href": "/sequence-files/IGVFFI4242BBXO/@@download/IGVFFI4242BBXO.fastq.gz",
"md5sum": "f0b538109d96cb5a92d8fecfdec72bdf",
"s3_uri": "s3://igvf-files/2025/04/09/890551bb-0ba1-44ea-940f-ff8bd1deec5d/IGVFFI4242BBXO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_2_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2049MUPB/",
"accession": "IGVFFI2049MUPB",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane2-CRISPR-L2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:04:27.129213+00:00",
"file_format": "fastq",
"file_size": 1112822853,
"href": "/sequence-files/IGVFFI2049MUPB/@@download/IGVFFI2049MUPB.fastq.gz",
"md5sum": "e708402d623f2c10a91df9ea80f6e888",
"s3_uri": "s3://igvf-files/2025/04/09/c14b9293-0508-4b4c-a62c-6cd20636e660/IGVFFI2049MUPB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_2_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7658RGOV/",
"accession": "IGVFFI7658RGOV",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane2-CRISPR-L2"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:29.706202+00:00",
"file_format": "yaml",
"file_size": 1449,
"href": "/configuration-files/IGVFFI7658RGOV/@@download/IGVFFI7658RGOV.yaml.gz",
"md5sum": "afe2aba7a550d813e7c7247f263e0e17",
"s3_uri": "s3://igvf-files/2025/04/09/0edd40f0-5b3d-415e-83e8-2f37308cb631/IGVFFI7658RGOV.yaml.gz",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane2-crispr-L2.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1333FBJB/",
"accession": "IGVFFI1333FBJB",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane2-CRISPR-L1"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:27.537955+00:00",
"file_format": "yaml",
"file_size": 1446,
"href": "/configuration-files/IGVFFI1333FBJB/@@download/IGVFFI1333FBJB.yaml.gz",
"md5sum": "2deb73110def4a077d3ee7fdcec52864",
"s3_uri": "s3://igvf-files/2025/04/09/db004b62-deac-4d8b-90ed-6cccd25925e9/IGVFFI1333FBJB.yaml.gz",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane2-crispr-L1.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8404CSTN/",
"accession": "IGVFDS8404CSTN",
"aliases": [
"charles-gersbach:hPA-measurement-set-perturbseq-10xlane2-GEX"
],
"preferred_assay_title": "Perturb-seq",
"status": "released"
}
],
"release_timestamp": "2025-05-16T16:07:10.567924+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM6449HHZS/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6449HHZS",
"aliases": [
"charles-gersbach:hPA-primary-cell-perturbseq-10xlane2"
],
"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": "2025-03-31T14:26:49.470724+00:00",
"summary": "gRNA sequencing for CRISPR activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "4ba2d578-e12a-40b4-9f06-82fad6b8b52a"
}