|
| Status |
Public on May 09, 2018 |
| Title |
RRBS_Heart_20wk_WT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Adult_WT_Heart
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl
tissue: Heart
age: 20wk
aav injection time: N_A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from mouse hepatocytes or from snap-frozen mouse tissues and incubated in lysis buffer (25 mM Tris-HCl (pH 8), 2 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation.
RRBS libraries were prepared as described (Boyle et al., 2012) and run on Hiseq 2500 (Illumina).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
genomic DNA
Big_table_all_samples_RRBS
|
| Data processing |
One-hundred-base pair paired-end sequencing reads from RRBS were trimmed and quality filtered by trim galore software (v0.3.3) using default parameters for RRBS with the following command:
trim_galore–rrbs–paired sample_R1.fastq.gz sample_R2.fastq.gz
BSMAP v2.74 (Xi and Li, 2009) was used for read alignment (genome build mm9) and extraction of single-base resolution methylation levels using the following commands:
bsmap -a sample_R1_val_1.fq.gz -b sample_R2_val_2.fq.gz -d mm9_AllGenome.fa -o bam_file -R -D C-CGG
python methratio.py -i “no-action” -p -g -z -o sample_trim_galore_mm9.fa.meth -d mm9_AllGenome.fa bam_file
Percent methylation was calculated for one-hundred-base pair tiles with a minimum coverage of 10 CpGs.
Genome_build: mm9
Supplementary_files_format_and_content: bed
|
| |
|
| Submission date |
Aug 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Klaus H Kaestner |
| E-mail(s) |
kaestner@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine
|
| Street address |
University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104-5156 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE85251 |
Postnatal DNA demethylation and its role in tissue maturation |
|
| Relations |
| BioSample |
SAMN05514289 |
| SRA |
SRX2004654 |
