{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9587OBVM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9587OBVM",
"aliases": [
"charles-gersbach:measurement-set-bulk-rna-control-ipsc-cm-rep1"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003090/",
"status": "released",
"term_name": "bulk RNA-seq assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9587OBVM](/measurement-sets/IGVFDS9587OBVM/) has sequence file(s): [IGVFFI9694LYUA](/sequence-files/IGVFFI9694LYUA/), [IGVFFI6063JLVO](/sequence-files/IGVFFI6063JLVO/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS9587OBVM/"
}
]
},
"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"
},
"control_for": [
{
"@id": "/measurement-sets/IGVFDS9314PRMO/",
"accession": "IGVFDS9314PRMO",
"aliases": [
"charles-gersbach:measurement-set-bulk-rna-chir4um-ipsc-cm-rep1"
],
"status": "released"
}
],
"creation_timestamp": "2024-10-23T19:18:44.999480+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3212TBUN/",
"accession": "IGVFDO3212TBUN",
"aliases": [
"charles-gersbach:human-donor-WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9694LYUA/",
"accession": "IGVFFI9694LYUA",
"aliases": [
"charles-gersbach:measurement-set-bulk-rna-control-ipsc-cm-rep1-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:28:47.584789+00:00",
"file_format": "fastq",
"file_size": 2913943199,
"href": "/sequence-files/IGVFFI9694LYUA/@@download/IGVFFI9694LYUA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/377ee81c-f88e-4cff-9b41-762b55cd4c89/IGVFFI9694LYUA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/tda17/Anglen_7276_210923B6_RNAseq/data/rna_seq/processed_raw_reads/Anglen_7276_210923B6_RNAseq/control.1.rna.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6063JLVO/",
"accession": "IGVFFI6063JLVO",
"aliases": [
"charles-gersbach:measurement-set-bulk-rna-control-ipsc-cm-rep1-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:28:48.862421+00:00",
"file_format": "fastq",
"file_size": 3056580485,
"href": "/sequence-files/IGVFFI6063JLVO/@@download/IGVFFI6063JLVO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/dbdbd405-b0fc-4722-a379-056f3014ff5a/IGVFFI6063JLVO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/tda17/Anglen_7276_210923B6_RNAseq/data/rna_seq/processed_raw_reads/Anglen_7276_210923B6_RNAseq/control.1.rna.R2.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7046PDMA/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "RNA-seq",
"protocols": [
"https://www.protocols.io/view/rna-seq-for-human-ipsc-cm-following-gsk3-inhibitio-kqdg32rb1v25"
],
"release_timestamp": "2024-12-10T00:24:35.096301+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7851SPEI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7851SPEI",
"aliases": [
"charles-gersbach:in-vitro-system-bulk-rna-control-ipsc-cm-rep1"
],
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-10-23T19:28:47.584789+00:00",
"summary": "RNA-seq",
"uuid": "92d5b244-e7fd-4505-b495-7ffe962d18dc"
}