|
| Status |
Public on Aug 01, 2014 |
| Title |
CD8-control |
| Sample type |
SRA |
| |
|
| Source name |
CD8+ T cells, untreated
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD8+ T cells
tissue: peripheral blood
disease status: healthy
age: 25-40 years
treatment: none
|
| Treatment protocol |
Cells were activated using T cell activation beads (Miltenyi) overnight and then treated for 24 h with 5ng/ml TGF-b, with 1µM SD-208 or left untreated.
|
| Growth protocol |
Cells were cultured in X-VIVO15 medium (Lonza).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with mirVana miRNA isolation kit (Ambion); subsequent fractionation of miRNAs was done by means of PAA gel electrophoresis.
Poly-A-tailing of the miRNAs; ligation of an RNA-adapter to the 5'-end; first-strand cDNA-synthesis using poly(T)-adapter; addition ot the complete flanking sequences while PCR-amplification; final purification of the PCR-product by means of agarose gel electrophoresis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
454 GS FLX |
| |
|
| Description |
Small RNA-Seq.
CD8+ T cells untreated.
|
| Data processing |
To process sequences, Perl scripts were used (available upon request).
Raw sequences were filtered and converted to FASTA format. Sequences were truncated at the first 7-mer of A's. Sequences shorter than 16 bases were omitted.
Adapter sequences were then removed.
Each sequence was aligned against all sequences in the miRbase. Sequences that did not hit any miRNA were computed further. Multiple sequences that mapped to one miRNA (due to sequencing errors) were then merged to build final number of read counts.
Different groups were then compared by normalizing the number of reads to 10000 reads in each group and in reads per million (RPM).
Genome_build: miRBase 15
Supplementary_files_format_and_content: File format: .txt. Contains the normalized number of reads (per 10000 and RPM) for each miRNA for respective groups in each column.
|
| |
|
| Submission date |
Apr 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Anoop Chandran P |
| E-mail(s) |
premachand_a@klinik.uni-wuerzburg.de
|
| Organization name |
University of Würzburg
|
| Street address |
Josef-schneiderstrasse
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9186 |
| Series (2) |
| GSE46322 |
Identification of miRNAs regulated by TGF-b in human CD8+ T cells (small RNA-seq) |
| GSE46325 |
Identification of miRNAs regulated by TGF-b in human CD8+ T cells |
|
| Relations |
| BioSample |
SAMN02055489 |
| SRA |
SRX271428 |
