|
| Status |
Public on Jan 09, 2020 |
| Title |
mESCs, BR2_WT_10min_tot |
| Sample type |
SRA |
| |
|
| Source name |
mESC (conditional Dicer mutant)
|
| Organism |
Mus musculus |
| Characteristics |
treatment duration (days): 8
rna fraction: 4sU preexisting (10 minutes)
biological replicate number: 2
cell type: mESC
genotype: WT
|
| Treatment protocol |
Loss of Dicer1 function was induced by culturing cells in mESC growth media supplemented with 800 nM tamoxifen ([Z]-4-Hydroxytamoxifen [4-OHT]).
Five million DTCM23/49 XY mESCs (WT and miRNA depleted) were seeded and allowed to grow to 70-80% confluency (approximately 1 day). 4sU was added to the growth medium (final concentration of 200 µM) and the cells were incubated at 37 ºC for 10 and 15 minutes
|
| Growth protocol |
Mouse DTCM23/49 XY embryonic stem cell lines (mESCs) were cultured in Knockout Dulbecco’s Modified Eagle Medium (D-MEM, Thermo Fisher, #10829-018) supplemented with 15% fetal bovine serum (FBS, Thermo Fisher, #16000-044), 1% antibiotic penicillin/streptomycin (Thermo Fisher, 15070063), Recombinant mouse LIF protein to a final concentration of 0.01% (Merck, #ESG1107) and 0.06 mM 2-Mercaptoethanol (Thermo Fisher, #31350-010), on 0.1% gelatin-coated cell culture dishes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol, according to manufacturer instructions. RNA was DNAse treated using RNeasy on column digestion according to manufacturer’s instructions. Total RNA libraries were prepared from 10 ng of DNase-treated preexisting and newly transcribed RNA using Ovation® RNA-Seq. reads were first mapped to mouse ribosomal RNA sequences with STAR v2.5.0. Reads that do not map to ribosomal RNA were then aligned to intronic and exonic sequences using STAR and quantified using RSEM.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
BR2_WT_10min_tot
4sU_TPM_table.txt
|
| Data processing |
4sU sequencing reads were first mapped to mouse ribosomal RNA sequences with STAR v2.5.0. Reads that do not map to ribosomal RNA were then aligned to intronic and exonic sequences using STAR and quantified using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: 4sU_TPM_table.txt contains the expression levels of transcript exons and introns (Transcripts Per Million, TPM).
|
| |
|
| Submission date |
Jan 08, 2020 |
| Last update date |
Jan 09, 2020 |
| Contact name |
Ana Marques |
| E-mail(s) |
anaclaudia.marques@unil.ch
|
| Organization name |
University of Lausanne
|
| Department |
Department of Computational Biology
|
| Street address |
Rue du Bugnon 27
|
| City |
Lausanne |
| ZIP/Postal code |
1005 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE143277 |
Translation is required for miRNA-dependent decay of endogenous transcripts. |
|
| Relations |
| BioSample |
SAMN13760696 |
| SRA |
SRX7520429 |
