 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 19, 2019 |
| Title |
RNA-seq WT 3 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Mus musculus |
| Characteristics |
embryo stage: E11.5
genotype: Dnmt3b +/+
strain: FVB
|
| Extracted molecule |
total RNA |
| 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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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 |
GPL24247 |
| Series (1) |
| GSE132952 |
Methylation and gene expression data from Dnmt3b+/+, Dnmt3b-/- and Dnmt3bCI/CI embryos harvested at E11.5 |
|
| Relations |
| BioSample |
SAMN12090558 |
| SRA |
SRX6090701 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
|
|
|
|
 |
