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Sample GSM2802794 Query DataSets for GSM2802794
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).
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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