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Series GSE198005 Query DataSets for GSE198005
Status Public on May 01, 2024
Title Genome-wide bisulfite sequencing (GWBS) and RNA-seq in hippocampus of Neil1- and Neil2 deficient mice
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary We report the bisulfite sequencing and RNA-seq in hippocampus of Neil deficient adult mice. By genome-wide bisulphite sequencing (GWBS) analysis, NEIL depletion mice (including Neil1-/-, Neil2-/- and Neil1-/- Neil2-/-) consistently displayed global hypo-methylation of 5mC in base resolution in CG context, as well as in gene feature regions including transcription start sites (TSS) in CHG and CHH context by compared to wild type. RNA-seq reveals differentially expressed genes are mainly overlapped with differential methylation. A subset of overlap genes is enriched in synaptic function. Together, NEIL1 and NEIL2 functionally promote DNA methylation and impact gene expression.
 
Overall design Examination of genome-wide 5mC and 5hmC in hippocampus of Neil deficient adult mice compared to wild type; investigation the correlation between methylaiton and gene expression.
 
Contributor(s) Yang M, Scheffler K, Bjoras M
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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
Phone 004746613633
Organization name Oslo University Hospital
Department Department of Microbiology, Rikshospitalet
Street address Sognsvannsveien 20
City Oslo
ZIP/Postal code 0372
Country Norway
 
Platforms (1)
GPL23479 BGISEQ-500 (Mus musculus)
Samples (16)
GSM5935611 G_WT_1
GSM5935612 G_WT_2
GSM5935613 G_Neil1_1
Relations
BioProject PRJNA813323

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE198005_RAW.tar 1.6 Gb (http)(custom) TAR (of BED, TXT)
GSE198005_data_normalization_count.txt.gz 1.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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