|
| Status |
Public on May 01, 2024 |
| Title |
T-cells allo-HSCT,d+52 ex vivo, 8-OHdG high, 1 [KMT126d52] |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
condition: high oxidative DNA damage
tissue: peripheral blood
cell type: primary T-cells
treatment: Allogeneic hematopoietic stem cell transplantation (allo-HSCT)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the innuPREP DNA/RNA Mini Kit (Analytik Jena AG, Jena, Germany); on column DNAse digestion was used to remove genomic DNA contamination (RNAse-Free DNase Set, Qiagen, Venlo, Netherlands). RNA was diluted in RNase free H2O to a maximum concentration of 200 ng/μl.
INVIEW transcriptome Explore (Eurofins)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
samples ex vivo allo-HSCT patients - no treatment ex vivo
|
| Data processing |
Adapters were clipped by trim_galore
Sequence reads were mapped by STAR aligner
Counting with featureCounts
Analysed using edgeR, normallized with TMM method
Supplementary files format and content: GRCh38
Supplementary files format and content: Tab-delimited normalized cpm
|
| |
|
| Submission date |
May 25, 2022 |
| Last update date |
May 01, 2024 |
| Contact name |
Chunguang Liang |
| E-mail(s) |
liang@biozentrum.uni-wuerzburg.de
|
| Phone |
09313184561
|
| Organization name |
Biozentrum
|
| Department |
Bioinformatics
|
| Lab |
Dr. Chunguang Liang
|
| Street address |
Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland
|
| City |
Würzburg 97074 |
| State/province |
Bayern |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE204782 |
Accumulating Oxidative DNA Damage in Reconstituting T-cells is Associated with Disease Relapse and Inferior Survival Following Allo-SCT [RNAseq in vivo] |
| GSE204783 |
Accumulating Oxidative DNA Damage in Reconstituting T-cells is Associated with Disease Relapse and Inferior Survival Following Allo-SCT |
|
| Relations |
| BioSample |
SAMN28657029 |
| SRA |
SRX15449725 |
