|
| Status |
Public on Jan 28, 2021 |
| Title |
MACE-seq_SRSF3_KD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MACE-seq_SRSF3_KD
|
| Organism |
Mus musculus |
| Characteristics |
cell line: P19
treatment: SRSF3_KD
molecule subtype: poly(A)+-selected
|
| Treatment protocol |
5 µg purified esiRNAs were transfected for 36 h using JetPRIME Transfection Reagent (Polyplus) according to the manufacturer’s instructions. EsiRNAs against GFP were used as controls.
|
| Growth protocol |
Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using the Trizol method.
For MACE-seq, total RNA was subjected to poly(A)+ selection and MACE library preparation according to Müller et al., 2014 PMID:25052703. MACE-seq libraries were sequenced on a Illumina HiSeq2000 platform obtaining 75-bp single-end reads (50 Million per replicate).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
library strategy: MACE (Massive Analysis of cDNA Ends)-seq
The analysis of MACE-seq data was performed as described in Müller et al., 2014 PMID:25052703.
Genome_build: mm10
Supplementary_files_format_and_content: All used PAS in P19 cells in .bed format
|
| |
|
| Submission date |
Jun 03, 2020 |
| Last update date |
Jan 28, 2021 |
| Contact name |
Michaela Müller-McNicoll |
| E-mail(s) |
[email protected]
|
| Phone |
+49 69 798 42079
|
| Organization name |
Goethe University Frankfurt
|
| Department |
Institute for Cell Biology and Neuroscience
|
| Lab |
RNA Regulation Group
|
| Street address |
Max-von-Laue-Str. 13
|
| City |
Frankfurt am Main |
| ZIP/Postal code |
60438 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE151722 |
MACE-seq of P19 cells after knockdown of Srsf3 and Srsf7 |
| GSE151724 |
iCLIP-seq, RNA-seq and MACE-seq studies in P19 cells |
|
| Relations |
| BioSample |
SAMN15095358 |
| SRA |
SRX8465060 |
