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Status |
Public on May 01, 2024 |
Title |
G_DK_2 |
Sample type |
SRA |
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Source name |
hippocampus
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Organism |
Mus musculus |
Characteristics |
strain background: C57Bl6N tissue: hippocampus age: post natal 6 months genotype/variation: Neil1-/- Neil2 -/-
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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.
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
BGISEQ-500 |
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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
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Submission date |
Mar 06, 2022 |
Last update date |
May 01, 2024 |
Contact name |
Mingyi Yang |
E-mail(s) |
mingyiy@medisin.uio.no
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Phone |
004746613633
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Organization name |
Oslo University Hospital
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Department |
Department of Microbiology, Rikshospitalet
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Street address |
Sognsvannsveien 20
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City |
Oslo |
ZIP/Postal code |
0372 |
Country |
Norway |
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Platform ID |
GPL23479 |
Series (1) |
GSE198005 |
Genome-wide bisulfite sequencing (GWBS) and RNA-seq in hippocampus of Neil1- and Neil2 deficient mice |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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