{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4582MPNU",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-rna-seq-batf3-overexpression"
],
"assay_titles": [
"RNA-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI9463EWKS](/alignment-files/IGVFFI9463EWKS/) has in progress subobject reference file [IGVFFI7213AWAM](/reference-files/IGVFFI7213AWAM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI9463EWKS/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI3680NTHN](/alignment-files/IGVFFI3680NTHN/) has in progress subobject reference file [IGVFFI7213AWAM](/reference-files/IGVFFI7213AWAM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI3680NTHN/"
},
{
"category": "NTR term ID",
"detail": "Treatment term for [451e1aee-b7f5-4a04-9fa5-672390a2506d](/treatments/451e1aee-b7f5-4a04-9fa5-672390a2506d/) has been newly requested. Treatments with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_treatment_term_id_check",
"path": "/treatments/451e1aee-b7f5-4a04-9fa5-672390a2506d/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI3725SWMW](/alignment-files/IGVFFI3725SWMW/) has in progress subobject reference file [IGVFFI7213AWAM](/reference-files/IGVFFI7213AWAM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI3725SWMW/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI3650PMFD](/alignment-files/IGVFFI3650PMFD/) has in progress subobject reference file [IGVFFI7213AWAM](/reference-files/IGVFFI7213AWAM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI3650PMFD/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI0822LWRZ](/alignment-files/IGVFFI0822LWRZ/) has in progress subobject reference file [IGVFFI7213AWAM](/reference-files/IGVFFI7213AWAM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI0822LWRZ/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI8140ZBAO](/alignment-files/IGVFFI8140ZBAO/) has in progress subobject reference file [IGVFFI7213AWAM](/reference-files/IGVFFI7213AWAM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI8140ZBAO/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3805WZUU](/primary-cells/IGVFSM3805WZUU/) 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/IGVFSM3805WZUU/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7232YAVV](/primary-cells/IGVFSM7232YAVV/) 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/IGVFSM7232YAVV/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0218YCAH](/primary-cells/IGVFSM0218YCAH/) 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/IGVFSM0218YCAH/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8821YQXI](/primary-cells/IGVFSM8821YQXI/) 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/IGVFSM8821YQXI/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6508DFUL](/primary-cells/IGVFSM6508DFUL/) 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/IGVFSM6508DFUL/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4633QTQY](/primary-cells/IGVFSM4633QTQY/) 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/IGVFSM4633QTQY/"
}
]
},
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},
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},
{
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}
],
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"data_use_limitation_summaries": [
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],
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],
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},
{
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"aliases": [
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],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9588OERW/",
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"aliases": [
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],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
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{
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"upload_status": "validated"
},
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],
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"content_type": "transcript quantifications",
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"upload_status": "validated"
},
{
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},
{
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"upload_status": "validated"
},
{
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],
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"content_type": "transcriptome alignments",
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"creation_timestamp": "2024-10-14T20:51:01.235184+00:00",
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"file_size": 1576094669,
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"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8-pSM7-IL-2-D1.star2.Aligned.out.sorted.bam",
"upload_status": "validated"
},
{
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"aliases": [
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"assembly": "GRCh38",
"content_type": "transcriptome alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-14T20:52:00.925571+00:00",
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"file_size": 1311182631,
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"upload_status": "validated"
},
{
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"aliases": [
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"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
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"accession": "IGVFDS0965VVJT",
"aliases": [
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],
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"status": "released"
},
{
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"aliases": [
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],
"file_set_type": "experimental data",
"status": "released"
},
{
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"aliases": [
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],
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"status": "released"
},
{
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"aliases": [
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],
"file_set_type": "experimental data",
"status": "released"
},
{
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"aliases": [
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],
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"status": "released"
},
{
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"aliases": [
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],
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],
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"lab": {
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"protocols": [
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],
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"status": "released"
}
],
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],
"accession": "IGVFSM6508DFUL",
"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [
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}
],
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"Item"
],
"status": "released",
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}
],
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]
},
{
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"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3805WZUU",
"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [
{
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"controlled_access": false,
"status": "released"
}
],
"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": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead for 14 days, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
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"status": "released",
"summary": "Treatment of 300 percent Antibody Coated Bead for 14 days",
"treatment_type": "protein"
}
]
},
{
"@id": "/primary-cells/IGVFSM4633QTQY/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4633QTQY",
"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
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"controlled_access": false,
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@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": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead for 14 days, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
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"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 300 percent Antibody Coated Bead for 14 days",
"treatment_type": "protein"
}
]
},
{
"@id": "/primary-cells/IGVFSM0218YCAH/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0218YCAH",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-activation-batf3-rep3"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
"certificate_identifier": "IP117-01",
"controlled_access": false,
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@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": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead for 14 days, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/451e1aee-b7f5-4a04-9fa5-672390a2506d/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 300 percent Antibody Coated Bead for 14 days",
"treatment_type": "protein"
}
]
},
{
"@id": "/primary-cells/IGVFSM7232YAVV/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7232YAVV",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-activation-batf3-rep2"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
"certificate_identifier": "IP117-01",
"controlled_access": false,
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@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": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead for 14 days, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/451e1aee-b7f5-4a04-9fa5-672390a2506d/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 300 percent Antibody Coated Bead for 14 days",
"treatment_type": "protein"
}
]
},
{
"@id": "/primary-cells/IGVFSM8821YQXI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8821YQXI",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-activation-batf3-rep1"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
"certificate_identifier": "IP117-01",
"controlled_access": false,
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@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": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead for 14 days, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/451e1aee-b7f5-4a04-9fa5-672390a2506d/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 300 percent Antibody Coated Bead for 14 days",
"treatment_type": "protein"
}
]
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-09-05T20:42:10.337751+00:00",
"summary": "RNA-seq: fold change over control, transcript quantifications, transcriptome alignments",
"uuid": "25476ba5-abdf-49e7-8a37-14a48fa7c22f",
"workflows": [
{
"@id": "/workflows/IGVFWF6270QWBB/",
"accession": "IGVFWF6270QWBB",
"name": "Gersbach GGR RNA-seq Pipeline",
"status": "released"
}
]
}