|
Status |
Public on May 01, 2024 |
Title |
T-cells allo-HSCT, d+105 ex vivo, 8-OHdG low, 5 [KMT94d105] |
Sample type |
SRA |
|
|
Source name |
peripheral blood
|
Organism |
Homo sapiens |
Characteristics |
condition: low 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)
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|
|
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
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|
|
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 |
SAMN28657021 |
SRA |
SRX15449733 |