|
| Status |
Public on Oct 19, 2017 |
| Title |
WT_Hippocampus_BS_8wk_Control_rep3 |
| 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).
|
| |
|
| 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 |
SAMN07731432 |
| SRA |
SRX3239285 |
