|
| Status |
Public on May 25, 2017 |
| Title |
HeLa acti rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: Actinonin (50 uM)
|
| Growth protocol |
DMEM plus L-glutamine and pyruvate with 10% inactivated FBS and penicillin and streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted from HeLa cells was extracted using RNA was extracted using TRIzol (Life Technologies) and purified by column using RNeasy Mini Kit (QIAGEN).
500ng of total RNA was enriched for Poly (A) RNA and then barcoded libraries for sequencing were prepared using the Lexogen mRNA Sense kit for Ion Torrent according to manufacturer’s standard protocol. Libraries were amplified 13 cycles and the quality of each library was checked on an Agilent Bioanalyzer DNA High Sensitivity chip. The libraries were pooled based on the concentration of each sample between 200-350bp, purified on a Pippin Prep gel, quantified by the Agilent Bioanalyzer and sequenced on an Ion Torrent Proton sequencer at 30x coverage depth .
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Data processing |
The reads obtained were first trimmed out to remove adaptor sequences and then mapped using a combined pipeline of TopHat2 (Kim et al., 2013a) and bowtie2 (Langmead and Salzberg, 2012) against the Human genome (GRCh37). HTSeq-count (Anders et al., 2015) was then used to obtain the counts of each gene. Differential expressed genes in each condition were identified using R/Bioconductor package edgeR (Robinson et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Normalized counts for all treatments
|
| |
|
| Submission date |
Jul 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Johan Auwerx |
| E-mail(s) |
admin.auwerx@epfl.ch
|
| Phone |
+41 216939522
|
| Organization name |
École Polytechnique Fédérale de Lausanne
|
| Department |
SV IBI NCEM
|
| Lab |
Integrative and Systems Physiology
|
| Street address |
Station 15
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17301 |
| Series (1) |
| GSE84631 |
RNA-seq analysis of mitochondrial stress |
|
| Relations |
| BioSample |
SAMN05420748 |
| SRA |
SRX1962102 |
