|
| Status |
Public on Dec 01, 2023 |
| Title |
patient vtr144 on d0 treated with 0bcg, vaccination via po administration |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral Blood
subject id: patient vtr144
treatment/time point: d0 treated with 0bcg, vaccination via po administration
molecule: Cytoplasmic RNA
cell type: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio
|
| Treatment protocol |
Autologuous CD4+ T cells cultured overnight with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio either in the presence of Danish BCG (Statens Serum Institut, Copenhagen, MOI 20:1), or medium alone.
|
| Growth protocol |
Blood was drawn into CPT tubes and PBMC isolated, aliquoted and frozen. Following thawing, CD4+ T cells were isolated using Miltenyi positive selection kits. Autologous monocyte-derived dendritic cells (MDDC) were prepared as described.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After overnight treatment with BCG/media, supernatants were harvested, frozen and stored for lysis and RNA extraction.
RiboZero v1
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
CACCAGG_vtr144_d0_0bcg_po
vtr144_d0_0bcg_po
|
| 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 30, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Richard Silver |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE224055 |
Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination [blood] |
|
| Relations |
| BioSample |
SAMN32961225 |
| SRA |
SRX19215642 |
