|
| Status |
Public on Jan 01, 2019 |
| Title |
nESC_sol_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
nESC, nucleoplasmic
|
| Organism |
Mus musculus |
| Characteristics |
originating cell line: E14
cell type: nESC
subcellular fraction: nucleoplasmic
|
| Treatment protocol |
Cellular fractionation was prepared as described (Pandya-Jones and Black, 2009), with minor changes. 1x10e7 cells (E14) were gently trypsinized from plate and centrifugation. As for isolation of nuclei, the lysate was layered on to 500 ul cold sucrose buffer.
|
| Growth protocol |
mESCs (E14) were cultured in serum-free N2B27 medium containing 2i (MEK and GSK inhibitor, PD0325901 and CHIR99021) and LIF. The nESC-to-EpiLC transition was conducted as described (Hayashi et al., 2011) with minor modifications. Briefly, mouse nESCs cells were plated at a density of 1x10e4 per cm2 in gelatin-coated plates with N2B27 medium containing activin A (20 ng/ml) and bFGF (12 ng/ml). The medium was changed every day. The converted EpiLCs were collected at day 3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HiSeq system (lllumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
ES_sol3_0
Processed data file: ES_genes.fpkm_table.txt
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
We trimmed and mapped reads to the mouse mm10 reference assembly (GRCm38) by the Tophat2 software (Kim et al., 2013). We used default parameters except that we reduced maximum insertion and deletion length to 2bp, and kept only uniquely mapping, “no mixed” and “no discordant” reads.
We quantified gene expression levels in each sample by cuffnorm (Trapnell et al., 2012) with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_genes.fpkm_table.txt: Tab-delimited text files include FPKM values for each replicate.
|
| |
|
| Submission date |
May 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bo Wen |
| E-mail(s) |
bowen75@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Institutes of Biomedical Sciences
|
| Street address |
130 DongAn Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE99366 |
RNA-seq of subcellular fractions from nESC and EpiLC |
|
| Relations |
| BioSample |
SAMN07172893 |
| SRA |
SRX2863221 |
