{
"@context": "/terms/",
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],
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],
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"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM5949AWIH](/primary-cells/IGVFSM5949AWIH/) 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/IGVFSM5949AWIH/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM1311HWOF](/primary-cells/IGVFSM1311HWOF/) 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/IGVFSM1311HWOF/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM5367RVVU](/primary-cells/IGVFSM5367RVVU/) 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/IGVFSM5367RVVU/"
}
]
},
"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"
},
"control_for": [],
"creation_timestamp": "2024-09-20T15:06:33.892618+00:00",
"donors": [
{
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],
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"status": "released",
"taxa": "Homo sapiens"
},
{
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],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO8565PQXZ/",
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"charles-gersbach:cd8-tcells-donor-12"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/IGVFFI3922QQPV/",
"accession": "IGVFFI3922QQPV",
"aliases": [
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],
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"content_type": "transcriptome alignments",
"creation_timestamp": "2024-10-14T21:02:00.991804+00:00",
"file_format": "bam",
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"href": "/alignment-files/IGVFFI3922QQPV/@@download/IGVFFI3922QQPV.bam",
"s3_uri": "s3://igvf-files/2024/10/14/794494fb-8888-4006-8401-a7e64f46656e/IGVFFI3922QQPV.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8.rnaseq.pSM73.znf217.d3.star2.Aligned.out.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI3234RYMD/",
"accession": "IGVFFI3234RYMD",
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"charles-gersbach:cd8-tcells-rna-seq-cas-ko-znf217-bam-rep2"
],
"assembly": "GRCh38",
"content_type": "transcriptome alignments",
"creation_timestamp": "2024-10-14T21:00:42.385431+00:00",
"file_format": "bam",
"file_size": 2796982247,
"href": "/alignment-files/IGVFFI3234RYMD/@@download/IGVFFI3234RYMD.bam",
"s3_uri": "s3://igvf-files/2024/10/14/eea4d823-1547-4252-a5ef-e3ed28a3a0cd/IGVFFI3234RYMD.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8.rnaseq.pSM73.znf217.d2.star2.Aligned.out.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI3628DFGJ/",
"accession": "IGVFFI3628DFGJ",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-znf217-bam-rep1"
],
"assembly": "GRCh38",
"content_type": "transcriptome alignments",
"creation_timestamp": "2024-10-14T20:59:34.263824+00:00",
"file_format": "bam",
"file_size": 2159921921,
"href": "/alignment-files/IGVFFI3628DFGJ/@@download/IGVFFI3628DFGJ.bam",
"s3_uri": "s3://igvf-files/2024/10/14/2d7652c0-a791-43fd-b7d4-3462bd9e8457/IGVFFI3628DFGJ.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8.rnaseq.pSM73.znf217.d1.star2.Aligned.out.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS3760HQCL/",
"accession": "IGVFDS3760HQCL",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-znf217-rep1"
],
"file_set_type": "experimental data"
},
{
"@id": "/measurement-sets/IGVFDS4636NLRL/",
"accession": "IGVFDS4636NLRL",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-znf217-rep2"
],
"file_set_type": "experimental data"
},
{
"@id": "/measurement-sets/IGVFDS3198NMHN/",
"accession": "IGVFDS3198NMHN",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-znf217-rep3"
],
"file_set_type": "experimental data"
}
],
"input_for": [
"/analysis-sets/IGVFDS9906UGWB/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [
"https://www.protocols.io/view/rnaseq-of-primary-human-t-cells-overexpressing-bat-c5pdy5i6",
"https://www.protocols.io/view/tfome-crisprko-screens-81wgbxk8olpk/v1"
],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
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"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
]
}
],
"release_timestamp": "2024-10-25T04:18:39.922343+00:00",
"sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, modified with CRISPR modifications, transfected with a guide library",
"samples": [
{
"@id": "/primary-cells/IGVFSM1311HWOF/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1311HWOF",
"aliases": [
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],
"classifications": [
"primary cell"
],
"construct_library_sets": [
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],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"sample_terms": [
{
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"@type": [
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"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM5367RVVU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5367RVVU",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-znf217-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7189YPQQ/"
],
"modifications": [
{
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"modality": "knockout"
}
],
"sample_terms": [
{
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"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5949AWIH",
"aliases": [
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],
"classifications": [
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"construct_library_sets": [
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],
"modifications": [
{
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"modality": "knockout"
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],
"sample_terms": [
{
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"@type": [
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"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
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"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-10-14T20:59:34.263824+00:00",
"summary": "knockout RNA-seq: transcriptome alignments",
"uuid": "dff2d881-73ed-413d-888f-11c0015c09cd",
"workflows": [
{
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"accession": "IGVFWF6270QWBB",
"name": "Gersbach GGR RNA-seq Pipeline"
}
]
}