|
| Status |
Public on Apr 02, 2024 |
| Title |
RNA-Seq of Mouse Embryonic Fibroblast: Transduced with shor-hairpin to KD RNF144b replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse embryonic fibroblasts
genotype: RNF144B KD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cells were washed with PBS, scrapped with 6M Urea and 200 mM Ammonium Bicarbonate and sonicated at 4ºC. 10 μl of each sample at 1 mg/ml was submitted for analysis. The samples were digested with Trypsin and LysC and 2 μg were analyzed by LC-MS/MS using a 90 min gradient in the Orbitrap Eclipse
2 μg were analyzed by LC-MS/MS using a 90 min gradient in the Orbitrap Eclipse. Raw MS files were processed in Proteome Discoverer version 2.3.0.523 (Thermo Scientific, Waltham, MA,) [44]. Samples have been searched against SP_Mouse database (June 2020), using the search algorithm Mascot v2.6 (http://www.matrixscience.com/). Peptides have been filtered based on FDR and only peptides showing an FDR lower than 5% have been retained.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Raw count matrix containing the raw counts for the different samples with the ensembl_id as rownames
|
| Data processing |
We performed a quality control on the 9 raw single-end reads samples using the nf-core/rnaseq (v. 3.10.1)
Raw FASTQ files were aligned to the GRCm38.p6 version of the reference mouse genome using STAR (v. 2.7.6a) with default parameters except for --sjdbOverhang 49, producing a set of 9 BAM files.
Genes were annotated using the GENCODE vM25 GTF file. We filtered out lowly expressed genes by discarding those that did not show a minimum reliable level of expression of 20 counts per million reads of the smallest library size, in at least all the samples of the smallest group, which was 3.
The DESeq2 package (v. 1.40.0) was used for the differential expression analysis. Surrogate variables were calculated with SVA.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files incudes raw counts for each sample
|
| |
|
| Submission date |
Apr 01, 2024 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Gerard Romero |
| E-mail(s) |
grspianus1999@gmail.com
|
| Organization name |
Universitat Pompeu Fabra
|
| Department |
Dpt of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS/UPF)
|
| Street address |
Doctor Aiguader, 88
|
| City |
Barcelona |
| State/province |
Catalonia |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE262951 |
The TP53-activated E3 ligase RNF144B is a tumour suppressor that prevents genomic instability |
|
| Relations |
| BioSample |
SAMN40629243 |
| SRA |
SRX24075487 |
