|
| Status |
Public on Aug 31, 2018 |
| Title |
Rrp40 mESC total RNA replicate 2 [CAGE-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Rrp40 mESC total RNA replicate 2
|
| Organism |
Mus musculus |
| Characteristics |
cell line: ES-E14TG2a
shRNA: RRP40
cell type: Embryonic stem cells
|
| Treatment protocol |
E14 mESC were transduced with lentiviral particles. After selection with puromycin, the cells were grown in 2i media without puromycin and differentiated as follows: 1.5 million cells in 30 ml differentiation media were hung in 20 microliters drops from the lids of p15 plates with PBS in the plate fro humidity. After two days, they were taken off the lid with PBS, let fall down in a falcon tube for 5 minutes. Then the liquid was removed and 26 ml of new differentiation media were added and the embryoid bodies and this media were split into two petri dishes for bacterial culture. 24 hours later, the embryoid bodies were harvested and lysed with TRIzol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol
CAGE libraries were prepared using the protocol by Takahashi et al. (doi: 10.1038/nprot.2012.005) with an input of 3 μg of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ES-E14TG2a
|
| Data processing |
The CAGE data was trimmed and quality controlled using FASTX Toolkit.
The trimmed reads were mapped using Bowtie against mm10.
Uniquely mapped reads were used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using Bedtools and bedGraphtoBigWig. The score represents strand specific per base genome coverage.
|
| |
|
| Submission date |
Jun 12, 2018 |
| Last update date |
Sep 02, 2018 |
| Contact name |
Evdoxia Karadoulama |
| E-mail(s) |
evka@mbg.au.dk
|
| Organization name |
Aarhus University
|
| Department |
Molecular Biology and Genetics
|
| Lab |
Torben Heick Jensen
|
| Street address |
C.F. Møllers Alle 3
|
| City |
Aarhus |
| ZIP/Postal code |
8000 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE115710 |
The RNA exosome contributes to gene expression regulation during stem cell differentiation [CAGE] |
| GSE115727 |
The RNA exosome contributes to gene expression regulation during stem cell differentiation |
|
| Relations |
| BioSample |
SAMN09405016 |
| SRA |
SRX4202552 |
