|
| Status |
Public on Jun 15, 2023 |
| Title |
RNA_410_rescue_exp_r4_tech2 |
| Sample type |
SRA |
| |
|
| Source name |
E14JU
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic stem cells
cell line: E14JU
strain: 129/Ola
genotype: wildtype
|
| 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 #E7405L) and strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep with Beads (NEB #E7765S)
NEBNext Ultra II Directional RNA Library Prep with Beads (NEB #E7765S) following the manufacturers protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
RNAseq_MCM2_rescue_gene_and_repeat_counts.txt.gz
|
| 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 M23) annotations with parameters --twopassMode Basic --twopass1readsN -1 --alignSJDBoverhangMin 10 and multimapping parameters -winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 for further repeats quantification
Gene level and repeat quantification at the subfamily level was obtained from processed bam files using the TEcount (version 2.1.3) program from the TEtoolkit suite, using the provided curated repeat annotations for mm10 (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/).
Assembly: mm10
Supplementary files format and content: RNAseq_MCM2_rescue_gene_and_repeat_counts.txt.gz is a tab separated text file with raw counts for genes (ENSEMBL ids) and repeats (Tecounts mm10 repeat ids)
|
| |
|
| Submission date |
Feb 01, 2023 |
| 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 |
GPL30172 |
| 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 |
SAMN33007566 |
| SRA |
SRX19247599 |
