{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3697TBRV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3697TBRV",
"aliases": [
"charles-gersbach:measurement-set-bulk-rna-control-ipsc-cm-rep3"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003090/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "bulk RNA-seq assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3697TBRV](/measurement-sets/IGVFDS3697TBRV/) 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/IGVFDS3697TBRV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3697TBRV](/measurement-sets/IGVFDS3697TBRV/) has sequence file(s): [IGVFFI4922RTAC](/sequence-files/IGVFFI4922RTAC/), [IGVFFI4743GQEZ](/sequence-files/IGVFFI4743GQEZ/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS3697TBRV/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6721GJUT](/in-vitro-systems/IGVFSM6721GJUT/) 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": "/in-vitro-systems/IGVFSM6721GJUT/"
}
]
},
"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/IGVFDS2590SMEJ/",
"accession": "IGVFDS2590SMEJ",
"aliases": [
"charles-gersbach:measurement-set-bulk-rna-chir4um-ipsc-cm-rep3"
],
"status": "released"
}
],
"control_type": "untreated",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:18:46.691239+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4922RTAC/",
"accession": "IGVFFI4922RTAC",
"aliases": [
"charles-gersbach:measurement-set-bulk-rna-control-ipsc-cm-rep3-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:28:52.520407+00:00",
"file_format": "fastq",
"file_size": 3034692319,
"href": "/sequence-files/IGVFFI4922RTAC/@@download/IGVFFI4922RTAC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/4ca4ee98-a15e-4ae7-9a5d-0e091f7a787d/IGVFFI4922RTAC.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.3.rna.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4743GQEZ/",
"accession": "IGVFFI4743GQEZ",
"aliases": [
"charles-gersbach:measurement-set-bulk-rna-control-ipsc-cm-rep3-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:28:53.956695+00:00",
"file_format": "fastq",
"file_size": 3196921697,
"href": "/sequence-files/IGVFFI4743GQEZ/@@download/IGVFFI4743GQEZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/7a889a6d-f737-48d8-bd6f-fa8522d2e095/IGVFFI4743GQEZ.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.3.rna.R2.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3461ZPPS/"
],
"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": "2024-12-10T00:24:35.301748+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6721GJUT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6721GJUT",
"aliases": [
"charles-gersbach:in-vitro-system-bulk-rna-control-ipsc-cm-rep3"
],
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/a62cea9b-2ae0-44e8-a6d6-81f419c56c71/",
"certificate_identifier": "IP117-03",
"controlled_access": false,
"status": "released"
}
],
"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": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-10-23T19:28:52.520407+00:00",
"summary": "untreated RNA-seq",
"uuid": "05996cf6-34cf-4e85-8fb8-0890d2e4fadc"
}