|
| Status |
Public on Aug 31, 2018 |
| Title |
Rrp40-EBd3-rep-3 [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Rrp40 EBd3 total RNA replicate 3
|
| Organism |
Mus musculus |
| Characteristics |
cell line: ES-E14TG2a
shRNA: RRP40
cell type: Embryonic stem cells differentiated for 3 days as embryoid bodies
|
| 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
Libraries were prepared, after rRNA-depletion using Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat; Illumina), using Illumina TruSeq Stranded mRNA LT Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Cells with a shRNA against RRP40 differentiated into embryoid bodies for three days in medium with FBS and without LIF or 2i.
|
| Data processing |
The RNA-Seq data was quality controled and trimmed using FastQC and Trimomomatics respectively.
The data was mapped using HISAT against mm10.
Uniquely mapped and properly paired 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 |
GPL21103 |
| Series (2) |
| GSE115714 |
The RNA exosome contributes to gene expression regulation during stem cell differentiation [RNA-Seq] |
| GSE115727 |
The RNA exosome contributes to gene expression regulation during stem cell differentiation |
|
| Relations |
| BioSample |
SAMN09404998 |
| SRA |
SRX4202574 |
