|
Status |
Public on Oct 19, 2017 |
Title |
WT_Hippocampus_BS_8wk_Control_rep2 |
Sample type |
SRA |
|
|
Source name |
Hippocampus
|
Organism |
Mus musculus |
Characteristics |
genotype: wild type background strain: C57BL/6 tissue: Hippocampus age: 8 week treatment: Control
|
Growth protocol |
Brain tissue was taken from wild-type mice maintained under standard housing conditions.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was isolated from each brain region at the indicated ages. WGBS libraries were constructed by using a similar method as previously described (Mo et al., 2015) except that NEXTflex methylated adapters (Bioo Scientific) were used. Briefly, DNA was sonicated to 200 bp using a Covaris S2. Bisulfite treatment was performed using EZ DNA Methylation-Gold kit (Zymo). Unmethylated lambda DNA (0.1-0.5%; Promega D1521) was spiked in to assess conversion rates.
|
|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
WT_Hippocampus_BS_8wk_Control.txt.gz
|
Data processing |
Reads were mapped to the mm9 genome using Bsmap (Xi et al., 2009). Duplicate reads were removed and only uniquely mapping reads were kept. Genome_build: mm9 genome + lambda genome (NC_001416.1) Supplementary_files_format_and_content: Each line indicates a cytosine in the genome with the following information listed for each column: Chromosome, nucleotide position, sequence context of cytosine (CG or CA), number of non-converted base-calls at this position (#C), total number of reads for the base at this position (# of C and T base-calls).
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|
|
Submission date |
Oct 02, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Hume Stroud |
Organization name |
UT Southwestern
|
Street address |
5323 Harry Hines Blvd
|
City |
Dallas |
State/province |
TX |
ZIP/Postal code |
75390 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE103213 |
Early-life gene expression in neurons modulates lasting epigenetic states. [Bisulfite-seq] |
GSE103214 |
Early-life gene expression in neurons modulates lasting epigenetic states. |
|
Relations |
BioSample |
SAMN07731433 |
SRA |
SRX3239284 |