{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8404CSTN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8404CSTN",
"aliases": [
"charles-gersbach:hPA-measurement-set-perturbseq-10xlane2-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 [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/"
},
{
"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": "Measurement set [IGVFDS8404CSTN](/measurement-sets/IGVFDS8404CSTN/) 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/IGVFDS8404CSTN/"
}
],
"WARNING": [
{
"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/"
},
{
"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": "Measurement set [IGVFDS8404CSTN](/measurement-sets/IGVFDS8404CSTN/) 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/IGVFDS8404CSTN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1645YFQD/",
"accession": "IGVFDS1645YFQD",
"aliases": [
"charles-gersbach:hPA-auxiliary-set-perturbseq-10xlane2-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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6102AFVS/",
"accession": "IGVFDS6102AFVS",
"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"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in many genes"
}
],
"control_for": [],
"creation_timestamp": "2025-03-28T17:18:29.301416+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
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"accession": "IGVFDO6921DDPB",
"aliases": [
"charles-gersbach:hPA-donor-34969"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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{
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"accession": "IGVFFI0306NDPI",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane2-GEX-L1-R1"
],
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"controlled_access": false,
"creation_timestamp": "2025-04-09T21:03:51.725703+00:00",
"file_format": "fastq",
"file_size": 3718842093,
"href": "/sequence-files/IGVFFI0306NDPI/@@download/IGVFFI0306NDPI.fastq.gz",
"md5sum": "1339685c141290069c408f542422c20d",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/GEX_2_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5393FNJJ/",
"accession": "IGVFFI5393FNJJ",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane2-GEX-L1-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:03:53.800006+00:00",
"file_format": "fastq",
"file_size": 9298924884,
"href": "/sequence-files/IGVFFI5393FNJJ/@@download/IGVFFI5393FNJJ.fastq.gz",
"md5sum": "74b3a27775cb183d1f0e9e8993c327a3",
"s3_uri": "s3://igvf-files/2025/04/09/9fc7db64-9bba-45b4-a5b0-a25256868d98/IGVFFI5393FNJJ.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_2_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5457COZZ/",
"accession": "IGVFFI5457COZZ",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane2-GEX-L2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:03:55.484510+00:00",
"file_format": "fastq",
"file_size": 3709713652,
"href": "/sequence-files/IGVFFI5457COZZ/@@download/IGVFFI5457COZZ.fastq.gz",
"md5sum": "73af98d70c959b074939f68c179a6ebe",
"s3_uri": "s3://igvf-files/2025/04/09/2a25abb9-ec6d-4156-8706-70d1e0e47936/IGVFFI5457COZZ.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_2_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9130ACWY/",
"accession": "IGVFFI9130ACWY",
"aliases": [
"charles-gersbach:hPA-Sequence-File-perturbseq-10xlane2-GEX-L2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-04-09T21:03:57.386552+00:00",
"file_format": "fastq",
"file_size": 9251980788,
"href": "/sequence-files/IGVFFI9130ACWY/@@download/IGVFFI9130ACWY.fastq.gz",
"md5sum": "a04137fc05245d9bbfa3f036b7620fe5",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/GEX_2_S2_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6111KMQB/",
"accession": "IGVFFI6111KMQB",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane2-GEX-L1"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:11.251516+00:00",
"file_format": "yaml",
"file_size": 1308,
"href": "/configuration-files/IGVFFI6111KMQB/@@download/IGVFFI6111KMQB.yaml.gz",
"md5sum": "749a6c431bc9fddcc641a5b06ed23193",
"s3_uri": "s3://igvf-files/2025/04/09/ac3fe32c-05ee-40b5-8322-99172225dc95/IGVFFI6111KMQB.yaml.gz",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane2-GEX-L1.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6324ZTES/",
"accession": "IGVFFI6324ZTES",
"aliases": [
"charles-gersbach:hPA-Seqspec-perturbseq-10xlane2-GEX-L2"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-09T21:13:13.750087+00:00",
"file_format": "yaml",
"file_size": 1305,
"href": "/configuration-files/IGVFFI6324ZTES/@@download/IGVFFI6324ZTES.yaml.gz",
"md5sum": "c91a16f0f606368964eca73399b2b11d",
"s3_uri": "s3://igvf-files/2025/04/09/f4ecb898-5238-4896-b90b-62dc2718174f/IGVFFI6324ZTES.yaml.gz",
"status": "released",
"submitted_file_name": "/work/rr151/SamAIM2neuro_data/AstrocytehPA-Seqspec-10xlane2-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": "2025-05-16T16:07:10.429023+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": "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": "2025-03-28T19:08:03.067459+00:00",
"summary": "CRISPR activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "4eb4081c-88c0-4bb1-8e6b-c552072ce477"
}