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Sample GSM2889313 Query DataSets for GSM2889313
Status Public on Dec 11, 2018
Title shBap1.rep1
Sample type SRA
 
Source name mouse embryonic stem cell
Organism Mus musculus
Characteristics cell type: mouse embryonic stem cell
cell line: E14
knockdown: shBap1
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 SAMN08177832
SRA SRX3471654

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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