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Sample GSM5935618 Query DataSets for GSM5935618
Status Public on May 01, 2024
Title G_DK_2
Sample type SRA
 
Source name hippocampus
Organism Mus musculus
Characteristics strain background: C57Bl6N
tissue: hippocampus
age: post natal 6 months
genotype/variation: Neil1-/- Neil2 -/-
Extracted molecule genomic DNA
Extraction protocol GWBS: total DNA was extracted from hippocampus of male mice using a AllPrep DNA/RNA/Protein mini-Kit, following by bisulfite treatment and library preparision. RNA-seq: RNA extracted by AllPrep DNA/RNA/Protein mini-Kit.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model BGISEQ-500
 
Data processing GWBS (bisulfite seq) -- The reads were aligned to reference mice genome GRCm38 , following to extract genome-wide 5mC in context of CG, CHG and CHH using Bismark tool. methylKit was used to quantify levels of methylated bases and to identify differently methylated cytosines, regions and promoters (DMC, DMR and DMP). The methylation profile and DMRs in gene feature regionsTSS, TES and gene body were analysed by a Python package HMST-Seq-Analyzer pipeline.
RNA-seq -- The clean reads were aligned to reference mouse genome mm10/GRCm38 by HISAT. The transcripts from all samples were futher assembled and merged using stingTie. The DESeq2 tool was used to normalize counts and identify the differentially expressed genes.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: 5mC percentage in CG context
Supplementary_files_format_and_content: transcript count table in FPKM
Supplementary_files_format_and_content: normalized count by DESeq2
 
Submission date Mar 06, 2022
Last update date May 01, 2024
Contact name Mingyi Yang
E-mail(s) mingyiy@medisin.uio.no
Phone 004746613633
Organization name Oslo University Hospital
Department Department of Microbiology, Rikshospitalet
Street address Sognsvannsveien 20
City Oslo
ZIP/Postal code 0372
Country Norway
 
Platform ID GPL23479
Series (1)
GSE198005 Genome-wide bisulfite sequencing (GWBS) and RNA-seq in hippocampus of Neil1- and Neil2 deficient mice
Relations
BioSample SAMN26492882
SRA SRX14391562

Supplementary file Size Download File type/resource
GSM5935618_DK_2.bed.gz 209.6 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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