|
Status |
Public on Dec 11, 2018 |
Title |
DZNep.rep1 |
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 |
SAMN08177772 |
SRA |
SRX3471634 |