|
| Status |
Public on Dec 31, 2017 |
| Title |
2i ES XX rep1 |
| Sample type |
SRA |
| |
|
| Source name |
2i cultured embryonic stem cells (XX)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: 2i cultured embryonic stem cells (XX)
|
| Growth protocol |
ESC XX derived from Oct-GFP (C57) background and maintained in ES medium contains DMEM (Merck Millipore) supplemented with 15% (v/v) fetal bovine serum (HyClone), 1 mM L-glutamine (Merck Millipore), 0.1 mMmercaptoethanol (Merck Millipore), 1% nonessential amino acid stock (Merck Millipore), penicillin/streptomycin (100×, Merck Millipore), nucleosides (100×, Merck Millipore), and 1000 U/ml LIF (Merck Millipore),and 2i.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The cells used for RNA-seq were collection after feeder-free treatment and washed by DPBS.RNA were exstracted by QIAGEN Allprep DNA/RNA mini Kit.
RNA libraray were constructed used KAPA stranded mRNA-seq kit illumina platform and sequenced at the Berry genomic corporation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq reads were aligned to the UCSC mouse genes (mm9) using Tophat (version 2.0.13). Only the uniquely mapped reads were retained for analysis in this study.
We used Cuffdiff (version 2.2.1) to calculate the expression abundance of each gene as fragments per kilobase per million mapped reads (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tab-delimited file showing gene expresssion levels with FPKM.
|
| |
|
| Submission date |
Nov 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaobai Zhang |
| E-mail(s) |
zhangxb@tongji.edu.cn
|
| Organization name |
Tongji University
|
| Street address |
1239 Siping Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE99588 |
Reduced diploidization and survival improvement of semi-cloned mice produced from androgenetic haploid embryonic stem cells |
|
| Relations |
| BioSample |
SAMN08026815 |
| SRA |
SRX3393342 |
