|
| Status |
Public on Aug 12, 2021 |
| Title |
II.2 [NGS02042] |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD3+ T cells
treatment: Candida-stimulated
genotype: CARD9 wild-type / CARD9 {delta}11
disease state: candida esophagitis, upper respiratory infections, hypogammaglobulinemia and low class-switched memory and plasmablast B cells
tissue: Blood
|
| Treatment protocol |
T cells from normal controls or patients were co-cultured with monocytes of one normal control in the presence of heat killed candida. After 3 days, T cell were enriched again to remove the monocytes and total RNA was extracted from the T cells for the RNA-sequencing (RNASeq) evaluation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ion AmpliSeq Transcriptome Human Gene Expression Kit (Life Technologies)
Targeted Sequencing Library (>20,000 human RefSeq genes)
Ion Torrent Proton sequencing system (Life Technologies)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Read mapping and counting were performed using the Ion Torrent Suite software v4.4.2
Read counts were variance stabilized (normalized) using DeSeq2
Genome_build: Homo sapiens (human) genome assembly GRCh37 (hg19)
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with variance-stabilized (normalized) counts for every gene and every sample
|
| |
|
| Submission date |
Aug 09, 2021 |
| Last update date |
Aug 12, 2021 |
| Contact name |
Julie E Niemela |
| E-mail(s) |
[email protected]
|
| Organization name |
NIH Clinical Center
|
| Department |
Dept. of Lab Medicine
|
| Lab |
Sequencing Lab
|
| Street address |
10 Center Dr
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE181718 |
RNASeq of Candida-stimulated CD3+ T-cells from individuals with CARD9 mutations and normal controls |
|
| Relations |
| BioSample |
SAMN20674243 |
| SRA |
SRX11678573 |
