|
| Status |
Public on Jun 15, 2023 |
| Title |
RNA_552_r1_POLE4-KO_exp |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14JU
strain: 129/Ola
genotype: Pole4KO
|
| Treatment protocol |
Samples were untreated.
|
| Growth protocol |
ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 degrees with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 5*10^6 cells using RNeasy Plus Mini Kit (Qiagen) and DNA was eliminated by treatment with the RNase-Free DNase Set (Qiagen). RNA was treated with the NEBNext rRNA Depletion kit (NEB #E6310) and strand-specific RNA libraries were prepared using the NEBNext Ultra Directional RNA Library Prep kit (NEB #E7420).
NEBNext Ultra Directional RNA Library Prep kit (NEB #E7420) following the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNAseq_Pole4_gene_and_repeat_counts.txt
|
| Data processing |
Sequences were trimmed for adapters and adapting filtering for low quality reads was performed with trimmomatic (version 0.39) with default parameters. Mapping (mm10) was performed with STAR (version 2.7.1a) using GENCODE (version M24) annotations with parameters --twopassMode Basic --twopass1readsN -1 --alignSJDBoverhangMin 10 and multimapping parameters -winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 for further repeats quantification
Gene level quantification was obtained from processed bam files using the featureCounts function in the Rsubread (version 2.0) R package and repeat subfamilies were quantified using the tool TEcount (version 2.1.3) ), using the provided curated repeat annotations for mm10 (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/).
Differential expression analysis of gene level and repeat subfamily level was performed with DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq_Pole4_gene_and_repeat_counts.txt: Tab-separated text file with raw counts for genes (ENSEMBL ids) and repeats (Tecounts mm10 repeat ids).
|
| |
|
| Submission date |
Feb 03, 2022 |
| Last update date |
Jun 15, 2023 |
| Contact name |
Anja Groth |
| E-mail(s) |
[email protected]
|
| Organization name |
Novo Nordisk Foundation Center for Protein Research
|
| Street address |
Blegdamsvej 3B
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE154390 |
Symmetric inheritance of parental histones governs epigenome maintenance and stem cell identity [RNA-seq] |
| GSE154391 |
Symmetric inheritance of parental histones governs epigenome maintenance and stem cell identity |
|
| Relations |
| BioSample |
SAMN25638840 |
| SRA |
SRX14036240 |
