|
| Status |
Public on Jun 24, 2024 |
| Title |
15A_Cre_2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts (immortalised)
|
| Organism |
Mus musculus |
| Characteristics |
treatment: transduced with phosphorylation deficient version of human HA-tagged CMTR1 (15A)
agent: transfected with vector encoding EF1alpha::Cre-GFP
cell type: embryonic fibroblasts
|
| Treatment protocol |
Cell were transfected with vector encoding EF1α::Cre-GFP and selected with 2µg/mL of puromycin after 24h for 48h. Cell were allowed to recover for 7 days prior to RNA extraction.
|
| Growth protocol |
Mouse embryonic fibroblasts were grown in Dulbecco's Minimum Essential Medium supplemented with 10% Fetal Bovine Serum, 100U/mL penicillin, 100µg/mL streptomycin and 0.5mg/mL G418. MEFs were cultured at 37 °C with 5 % CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using GeneJET RNA Purification Kit (ThermoFisher Scientific)
Sequencing libraries were prepared by Novogene using ribosomal RNA depletion. The libraries were sequenced by Novogene using NovaSeq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing was performed with a read length of 2×150 bp using a high output kit on Illumina NextSeq 500
The quality of sequencing reads was checked using FastQC and the adaptors were trimmed using Cutadapt (Martin, 2011)
The trimmed reads were aligned to the mouse genome assembly GRCm38/mm10 using STAR
The PCR duplicates from the mapped reads were removed using Picard (Wysoker et al., 2013)
Each reads per gene was quantified using htseq (Anders et al., 2015)
Assembly: mm10
Supplementary files format and content: Each reads per gene file contains a tab delimited table of reads per gene counted, the first column indicates the ensembl gene id, the second column shows the read count
|
| |
|
| Submission date |
Apr 04, 2022 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Radoslaw Lukoszek |
| E-mail(s) |
rlukoszek@gmail.com
|
| Organization name |
University of Potsdam
|
| Street address |
Karl-Liebknecht-Strasse 24-25
|
| City |
Potsdam |
| ZIP/Postal code |
14476 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE200103 |
CK2 phosphorylation of cap methyltransferase CMTR1 promotes RNAPII interaction |
|
| Relations |
| BioSample |
SAMN27284927 |
| SRA |
SRX14721881 |
