|
| Status |
Public on Nov 18, 2019 |
| Title |
RNA-seq.Unsorted-no2DG_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mESCs
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse embryonic stem cells (mESCs)
condition: no 2DG
|
| Treatment protocol |
In RNA-seq, Culture media was supplemented with 4mM 2-DG for 4 days to induce NELFA for reporter mESC. 0.4 µg/ml of Dox was used to induce NELFA for Dox-inducible mESC for 16 hours.
|
| Growth protocol |
mESCs were cultured on gelatin coated cell culture dishes with knockout DMEM supplemented with serum, LIF and 2i.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: Total RNA was extracted using TRI-reagent and purified using the Direct-zol RNA MiniPrep Kit by Zymo.
RNA-seq: 1µg of total RNA was used as input for library preparation; first, ribosomal depletion was carried using the NEBNext rRNA depletion kit (Cat: E6310S) and RNA-seq libraries were constructed using the NEBNext RNA Ultra II directional library kit (Cat: E7760S) as per manufacturer’s instructions. Average peak distribution of purified libraries was assessed on an Agilent Technologies 2100 Bioanalyzer using a DNA 1000 kit (Cat: 5067-1504). The concentration of adapter-ligated libraries was subsequently assessed using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824). Individual libraries were then pooled in equimolar amounts to a final concentration 5nM in preparation for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were trimmed to remove the adapter sequences and low quality bases using Trim_Galore (v0.4.2_dev).
For RNA-seq, reads mapping to the mouse GRCm38 reference genome, guided by the vM9 gene model from the GENCODE project, and gene expression quantification were carried out by RSEM pipeline. Repetitive elements expression quantification was carried out by RepEnrich pipeline, where repeat annotation in mm10 was obtained from the UCSC genome browser track repeatMasker. Differential gene and Repetitive elements expression was called using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: EXCEL file contains counts and deseq2 results for differential gene and TE expression analyses.
|
| |
|
| Submission date |
Apr 25, 2018 |
| Last update date |
Nov 18, 2019 |
| Contact name |
Zhenhua hu |
| E-mail(s) |
zhhu@imcb.a-star.edu.sg
|
| Phone |
65869644
|
| Organization name |
IMCB, A*STAR
|
| Street address |
31 Biopolis drive
|
| City |
Singapore |
| State/province |
singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE113671 |
NELFA is a novel regulator of the 2C-like state |
|
| Relations |
| BioSample |
SAMN08981698 |
| SRA |
SRX3994239 |
