|
| Status |
Public on Dec 01, 2023 |
| Title |
patient 02BAL014, uninfected_in_vitro, id_group |
| Sample type |
SRA |
| |
|
| Source name |
Bronchoalveolar Lavage (BAL) fluid
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bronchoalveolar Lavage (BAL) fluid
subject id: patient 02BAL014
treatment: uninfected_in_vitro
group: id_group
molecule: Cytoplasmic RNA
|
| Treatment protocol |
Frozen stocks of virulent Mtb strain H37Rv (#NR-123, BEI resources, Manassas VA) were thawed, cleared of bacterial clumps, and suspended in infecting medium. BAL cells were cultured with H37Rv (3:1 MOI) or medium alone and incubated at 37degC for twenty-four hours.
|
| Growth protocol |
Bronchoscopy with BAL was performed by instillation and recovery of up to eight 30 mL aliquots of saline. Following centrifugation, cell pellets were combined, counted and aliquoted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were flash-frozen and stored at -80 for eventual RNA extraction.
RiboZero v1
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
02BAL014_mediarested_id
AGCTCGC-GGTAGTA_02BAL014_mediarested_id
|
| Data processing |
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4.b
Gene counts quantitated with Subread:featureCount 1.45 with CPM transformation added with custom Rscripting.
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts-per-million in tab-delimitted text format
|
| |
|
| Submission date |
Jan 29, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Richard Silver |
| E-mail(s) |
rfs4@case.edu
|
| Organization name |
Case Western Reserve University and the Louis Stokes Cleveland VA Medical Center
|
| Department |
Division of Pulmonary, Critical Care and Sleep Medicine
|
| Street address |
10900 Euclid Ave
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE223999 |
Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination |
|
| Relations |
| BioSample |
SAMN32955013 |
| SRA |
SRX19212359 |
