|
| Status |
Public on Feb 19, 2021 |
| Title |
S27 |
| Sample type |
SRA |
| |
|
| Source name |
iPSCs_monoallelic mutant 1_control
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: induced pluripotent stem cells (iPSCs)
passage: 20-25
genotype: monoallelic mutant 1
treatment: none (normal condition)
|
| Treatment protocol |
For starvation cells were treated 2 hour with medium containing DMEM F12, FGF, TGFß,human activin A at the concentration as in FTDA, but lacking insulin, transferin, selenous acid, lipids and human serum albumin. Etoposide treatment was performed for 2 hours with 30 uM etoposide.
|
| Growth protocol |
iPS cells were grown in FTDA medium as previously described by Frank et al. 2012.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Direct-Zol RNA purification kit (Zymo Research) as recommended by manufacturer.
3'-endRNA libraries were prepared for sequencing using Lexogen QuantSeq 3' mRNA-Seq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
K002000301_100591_S27_L008
|
| Data processing |
Sequenced reads were mapped with STAR v2.2.2a with parameters --outFilterMatchNminOverLread 0.4 --outFilterScoreMinOverLread 0.4 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1
Reads were mapped to exons were counted by htseq-count using the following parameters: minimum alignment 30
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts (output of htseq-count), bigWig files (strant-specific)
|
| |
|
| Submission date |
Aug 14, 2019 |
| Last update date |
Feb 19, 2021 |
| Contact name |
Yulia Kargapolova |
| Organization name |
Cologne University
|
| Department |
CMMC
|
| Lab |
AG Papantonis
|
| Street address |
Robert-Koch-Straße 21
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE135832 |
Impaired CHD6 function links misregulation of autophagy and DNA damage response to premature ageing [RNA-Seq] |
| GSE161120 |
Impaired CHD6 function links misregulation of autophagy and DNA damage response to premature ageing |
|
| Relations |
| BioSample |
SAMN12572444 |
| SRA |
SRX6714241 |
