|
| Status |
Public on Dec 11, 2018 |
| Title |
shBahd1.rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cell
cell line: E14
knockdown: shBahd1
|
| 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 |
Illumina HiSeq 3000 |
| |
|
| 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 files 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 |
GPL21493 |
| Series (2) |
| GSE108087 |
Epigenetic control of genes and transposable elements [Knockdown RNA-seq] |
| GSE108091 |
Epigenetic control of genes and transposable elements |
|
| Relations |
| BioSample |
SAMN08177840 |
| SRA |
SRX3471653 |
