|
| Status |
Public on May 30, 2016 |
| Title |
AGS1 [L2549_H2O2] |
| Sample type |
SRA |
| |
|
| Source name |
fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: AGS
passages: passages 4-11
tissue: skin biopsies
agent: hydrogen peroxide (400 µM)
|
| Treatment protocol |
Oxidative stress was induced by adding hydrogen peroxide (400 µM) to the medium followed by incubation for 10 min at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from fibroblasts was extracted with the RNeasy Mini Kit (Qiagen) followed by DNase I digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols. Strand specific RNA-Seq (dUTP method)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
L2549_H2O2
|
| Data processing |
For data analyses a splice junction library with a length of 120 nucleotides (60+60) per splice junction was created based on known exon-exon junctions according to the Ensembl Genes annotation (v. 67, May 2012)
Alignment of the reads to the hg19 transcriptome was performed with pBWA
A counts-per-gene table was created based on the overlap of the uniquely mapped reads with the Ensembl Genes annotation for hg19, using BEDtools (v. 2.11)
RPKM (reads per kilobase per million reads) values were calculated based on the raw read counts and used as a measure of absolute expression levels.
Genome_build: hg19
Supplementary_files_format_and_content: excel file with RPKM counts table
|
| |
|
| Submission date |
Jul 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Min Ae Lee-Kirsch |
| E-mail(s) |
MinAe.Lee-Kirsch@uniklinikum-dresden.de
|
| Organization name |
Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden
|
| Department |
Klinik für Kinder- und Jugendmedizin
|
| Lab |
Molekulare Pädiatrie
|
| Street address |
Fetscherstr. 74
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE59233 |
Impaired DNA damage metabolism promotes autoimmunity in TREX1 deficiency |
|
| Relations |
| BioSample |
SAMN02905522 |
| SRA |
SRX648338 |
