|
| Status |
Public on Nov 07, 2019 |
| Title |
totalRNA_C_1_0h |
| Sample type |
SRA |
| |
|
| Source name |
RNA_C_0h
|
| Organism |
Mus musculus |
| Characteristics |
strain: BDF1
cell type: derived ESC
genotype/variation: wild type
treatment: Actinomycin D treatment for 0h. ERCC spike-in added.
|
| Treatment protocol |
ESCs were treated with Actinomycin D at 5μg/ml final concentration.
|
| Growth protocol |
ESC derived from blastocysts (BDF1 strain) were cultured in ESC medium: DMEM (Gibco),15% fetal bovine serum (Hyclone), nucleosides (100×),1 mM l-glutamine,1% nonessential amino acid stock, 0.1 mM mercaptoethanol, 1,000 U/ml LIF (Merk Millipore), 3 m CHIR99021 (S2924; Selleck) and 1 M PD0325901 (S1036; Selleck).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was obtained from at least 5×10^5 ESCs via RNeasy Mini Kit extraction(Qiagen).
For total RNA (rRNA erased), 1μg total RNA were used for RNA-seq with the KAPA RiboErase Kit (Roche) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
totalRNA_C_1_0h_A001
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
For RNA half-life test, gene and ERCC reads count were calculated using Htseq-count (v 0.6.0).
Gene counts were normalized by ERCC normalizing factor which got from estimateSizeFactorsForMatrix for ERCC counts using DESeq2 tools.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include ERCC normalized counts at different treated time were assembled in text files.
|
| |
|
| Submission date |
Mar 04, 2019 |
| Last update date |
Nov 07, 2019 |
| Contact name |
You Wu |
| E-mail(s) |
wuyou@tongji.edu.cn
|
| Organization name |
tongji university
|
| Department |
school of life science and technology
|
| Street address |
1239 siping road
|
| City |
shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE127790 |
Nuclear exosome targeting complex core factor Zcchc8 regulates the degradation of LINE1 RNA in early embryos and embryonic stem cells |
|
| Relations |
| BioSample |
SAMN11050351 |
| SRA |
SRX5460530 |
