|
| Status |
Public on Dec 11, 2018 |
| Title |
DZNep.rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cell
cell line: E14
treatment: DZNep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM13) transcriptome using Bowtie2 (version 2.2.5) and RSEM 。
The gene expression level was calculated by using EDASeq GC-normalize method
Genome_build: mm10
Supplementary_files_format_and_content: csv file with GC-normalised read counts from RSEM
|
| |
|
| Submission date |
Dec 14, 2017 |
| Last update date |
Dec 11, 2018 |
| Contact name |
Jiangping He |
| E-mail(s) |
he_jiangping@grmh-gdl.cn
|
| Organization name |
Guangzhou Institutes of Biomedicine and Health (GIBH), CAS
|
| Street address |
Kai yuan avenue 190
|
| City |
GuangZhou |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE108090 |
Epigenetic control of genes and transposable elements [inhibitor RNA-seq] |
| GSE108091 |
Epigenetic control of genes and transposable elements |
|
| Relations |
| BioSample |
SAMN08177771 |
| SRA |
SRX3471635 |
