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Sample GSM5160111

Query DataSets for GSM5160111

Status

Public on May 15, 2021

Title

TC1-EGFP 4sU-10nM-4h

Sample type

SRA

Source name

mESC

Organism

Mus musculus

Characteristics

cell line: TC1-EGFP
cell type: mESC cultured in serum/lif + 10 nM PlaB medium

Extracted molecule

total RNA

Extraction protocol

DNA and RNA extracted according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina). 4sU-seq libraries preparation using TruSeq Stranded Total RNA Sample Prep Kits (Illumina). ATAC-seq Library Preparation is according to insructions of Corces et al. Nature Methods 2017.

Library strategy

OTHER

Library source

transcriptomic

Library selection

other

Instrument model

HiSeq X Ten

Data processing

Library strategy: 4sU-seq
For PolyA(+) RNA-seq, Trimmomatic software was used to trim the adapters. Hisat2 software was used for the alignment to the mm10 reference genome with default parameters. For 4sU-seq data, All reads were trimmed by Trimmomatic. The reads which were not aligned to the mm10 repeats or BK000964.3 (rRNA) sequence were used to mapped to the mm10 reference genome with the same commands in PolyA(+) RNA-seq analysis. The ATAC-seq data were processed using ATAC-seq pipeline from Kundaje lab, including trimming, alignment, filtration and quality control.
The expression count matrix was obtained by FeatureCounts.
Data were normalized by total mapped reads of each library (CPM: count per million).
Genome_build: mm10

Submission date

Mar 11, 2021

Last update date

May 15, 2021

Contact name

Min Yang

E-mail(s)

yangmean@pku.edu.cn

Phone

15210364662

Organization name

Peking University