 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 08, 2017 |
| Title |
sham4 (RRBS) |
| Sample type |
SRA |
| |
|
| Source name |
rat hippocampus
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: hippocampus
treatment: sham
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Geome DNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of DNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Qubit RNA assay (Life Technologies, NY, USA) and gel electrophoresis
Reduced representation bisulfite sequencing (RRBS) libraries were constructed as described previously with some modifications (Chen, P.Y. et al. Physiol Genomics 45, 565-576). Briefly, about 1,000 ng genomic DNA was digested with the MspI enzyme. Digested DNA was then purified, end-repaired, and adenylated, followed by ligation to Illumina TruSeq barcode adapters (Illumina Inc, CA, USA). Fragments of 150-300 bp in size were selected, bisulfite-treated, and sequenced using an Illumina Hiseq 2500 System (Illumina Inc, CA, USA).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
replicate 1
|
| Data processing |
Reads were trimmed to remove the adapter sequences and low quality bases.
Bisulfite-converted reads were aligned to aligned to rat genome (UCSC assembly 5.0) using using the bisulfite aligner BS Seeker2, which utilizes the short read aligner Bowtie. As bisulfite treatment converted unmethylated cytosines (Cs) to thymines (Ts), we estimated the methylation level at each covered cytosine by methylation percentage which was calculated as NC/(NC + NT), where NC is the number of methylated reads and NT is the number of unmethylated reads
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files including the methylation level of cytosines in CpG, CHH and CHG context. The 8 fields in the files are (1) chromosome, (2) nucleotide on Watson (+) strand, (3) position, (4) context (CG/CHG/CHH), (5) dinucleotide-context (CA/CC/CG/CT), (6) methylation-level = #_of_C / (#_of_C + #_of_T)., (7) #_of_C (methylated C, the count of reads showing C here), (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)
|
| |
|
| Submission date |
Jan 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xia Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
UCLA
|
| Department |
IBP
|
| Street address |
2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE64984 |
DNA methylation profile for male SD rats with and without traumatic brain injury (TBI) by RRBS |
| GSE64986 |
Gene expression and DNA methylation profiles for male SD Rats with and without traumatic brain injury |
|
| Relations |
| BioSample |
SAMN03284608 |
| SRA |
SRX843454 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1585502_sham4.CGmap.txt.gz |
42.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
