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Sample GSM3897443 Query DataSets for GSM3897443
Status Public on Aug 19, 2019
Title RRBS 3bKO 1
Sample type SRA
 
Source name whole embryo
Organism Mus musculus
Characteristics embryo stage: E11.5
genotype: Dnmt3b -/-
strain: FVB
Extracted molecule genomic DNA
Extraction protocol For RRBS, genomic DNA was isolated from two independent Dnmt3b+/+, Dnmt3b-/- and Dnmt3bCI/CI embryos and tumor cell line using phenol/chloroform. For RNA-seq, total RNA was isolated by trizol from three independent Dnmt3b+/+; Dnmt3b-/- and Dnmt3bCI/CI embryos.
The RRBS libraries were prepared and sequenced on an Illumina HiSeq2500 sequencer. RNA-seq was performed on NovaSeq 6000 platform using paired-end 150bp runs.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2500
 
Data processing The input sequences were trimmed using trimmomatic. Quality control was performed before and after trimming using FastQC. The input reads were aligned to the reference genome (mm10) using bsmap. Methylation calling was performed using Methyldackel (v 0.3.0.1). Differentially methylated regions (DMRs) were determined by Metilene. DMRs were determined based on average DMC methylation change of 30 percent or greater, p-values (MWU) < 0.05, with a minimum of three DMCs represented in a maximum distance of 200bp.
For RNA-seq, trimmed sequencing data were first aligned to mm10 reference genome using STAR aligner. RNA-seq data with minimum mapped quality 50 were quantitated using the RNA-seq quantitation pipeline in SeqMonk software. Genome version used was Mus musculus GRCm38 (08/06/2012). DeSeq2 was used to calculate differential expression. For differentially expressed genes, only genes with a fold change ≥ 2 and a p-value < 0.05 were considered to be significant.
Genome_build: mm10
 
Submission date Jun 18, 2019
Last update date Aug 19, 2019
Contact name Rene Opavsky
E-mail(s) ropavsky@ufl.edu
Phone 3522948599
Organization name University of FLORIDA
Department Anatomy and cell biology
Street address 2033 Mowry rd, CGRC r..265
City Gainesville
State/province FL
ZIP/Postal code 32610
Country USA
 
Platform ID GPL17021
Series (1)
GSE132952 Methylation and gene expression data from Dnmt3b+/+, Dnmt3b-/- and Dnmt3bCI/CI embryos harvested at E11.5
Relations
BioSample SAMN12090564
SRA SRX6090695

Supplementary file Size Download File type/resource
GSM3897443_RRBS_3bKO_1.bigwig 10.9 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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