|
| Status |
Public on Oct 28, 2021 |
| Title |
KO_2_MommeD |
| Sample type |
SRA |
| |
|
| Source name |
mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESC
strain: FVB/NJ
genotype: Morc3D41/D41
|
| Growth protocol |
All mESC lines were cultured in serum conditions (Knockout DMEM (10829-018; Gibco), 10% FBS (DE14-801F; BioWhittaker), NEAA (11140; Gibco), L-Glutamine (25030-123; Gibco), Sodium Pyruvate (11360; Gibco), 2-Mercaptoethanol (31350; Gibco) and Leukemia Inhibitory Factor (ESG1107; Millipore)) plus MEK inhibitor PD0325901 (1 mM) and GSK3 inhibi- tor CHIR99021 (3 mM) (Axon Medchem) on 0.1% gelatin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with QIAzol (5346994; Qiagen) followed by isopropanol precipitation protocol.
Libraries were sequenced with 100bp paired-end (PE) on BGI
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The adaptors of RNA-seq samples were removed by the tool trim_galore using default parameters for paired-end Illumina reads, after, a quality filtering was driven by the same software and the results were supervised using FastQC
The remained reads were mapped to mm10 mouse genome using STAR aligner with the following parameters –outputMultimapperOrder random –twopassMode Basic.
the duplicated reads were marked by Piccard tools and then, the quantification versus GENCODE MV16 was driven by htseq-count v0.91
Genome_build: mm10
Supplementary_files_format_and_content: RNA_seq_counts_genes_MommeD.txt
Supplementary_files_format_and_content: RNA_seq_counts_TE_MommeD.csv
|
| |
|
| Submission date |
May 05, 2021 |
| Last update date |
Jan 12, 2023 |
| Contact name |
Lucia Daxinger |
| E-mail(s) |
[email protected]
|
| Organization name |
Leiden Univeristy Medica Center
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| ZIP/Postal code |
2333ZA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE173910 |
Morc3 silences endogenous retroviruses in mouse embryonic stem cells [Morc3_mESCs_RNAseq] |
| GSE173917 |
Morc3 silences endogenous retroviruses in mouse embryonic stem cells |
|
| Relations |
| BioSample |
SAMN19022944 |
| SRA |
SRX10783392 |
