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| Status |
Public on Dec 31, 2018 |
| Title |
DHA_hippocampus_rep1 [RRBS] |
| Sample type |
SRA |
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| Source name |
DHA_hippocampus
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
gender: male
fed with: DHA for 6 wks
tissue: hippocampus
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| Treatment protocol |
Rats were fed with fructose and/or DHA for 6 weeks
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| 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).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
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| 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)
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| Submission date |
Jan 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xia Yang |
| E-mail(s) |
[email protected]
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| Organization name |
UCLA
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| Street address |
610 Charles E. Young Dr. East
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (2) |
| GSE89175 |
Genome-wide transcriptomic and epigenomic study of DHA in rat hypothalamus and hippocampus [RRBS] |
| GSE89176 |
Genome-wide transcriptomic and epigenomic study of DHA in rat hypothalamus and hippocampus |
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| Relations |
| BioSample |
SAMN03280102 |
| SRA |
SRX835008 |
| SRA |
SRX2337189 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1581157_Hippo_DHA_rep1.txt.gz |
53.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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