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Series GSE134748 Query DataSets for GSE134748
Status Public on Jul 31, 2022
Title Communication between corpus callosum and SVZ mediated by locally controlled circadian clocks during demyelination
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We report two sets of potential circadian clock target genes by high-throughput transcriptome profiling (RNA-sequencing): one set from the corpus callosum of the adult mouse brain and the other set from adult neural stem cell cultured from the SVZ (neurospheres) of the mouse brain. First, the corpus callosum was dissected from three adult wild-type and two Bmal1 knockout (Bmal1-/-) mice, mRNA profiles were generated by deep sequencing using BGISEQ-500 RNA-Seq platform. The sequence reads that passed quality control were analyzed: we mapped more than 21 million total clean reads, more than 96% total Mapping Ratio, more than 86% Uniquely Mapping Ratio per sample to mouse genome. qRT-PCR validation with primers covering at least 3 known housekeeping genes and at least 5 well-known circadian clock genes were performed with SYBR Green assay. 103 differentially expressed genes (DEGs) were identified in the corpus callosum of Bmal1-/- mice (58 up-regulated and 45 down-regulated genes; |log2FC| > 1 & adjusted P-value < 0.05). Hypergeometric test revealed that potential functions of circadian clock target genes in the corpus callosum are secreted proteins as signaling molecules. For the second set of data, neurospheres were cultured from the SVZ of three adult wild-type and three adult Bmal1-/- mice, mRNA profiles were generated by deep sequencing using BGISEQ-500 RNA-Seq platform. The sequence reads that passed quality control were analyzed: we mapped more than 28 million total clean reads, more than 97% total Mapping Ratio, more than 68% Uniquely Mapping Ratio per sample to mouse genome. qRT-PCR validation with at least 3 known housekeeping genes and at least 5 well-known circadian clock genes using SYBR Green assay. 30 DEGs were identified in neurospheres cultured from Bmal1-/- mice (17 up-regulated and 13 down-regulated genes; |log2FC| > 1 & adjusted P-value < 0.05). Gene Set Enrichment Analysis (GSEA) revealed that potential circadian clock associated functions in the SVZ (neurospheres) are controlling diverse signal transductions.
 
Overall design mRAN profiles in the corpus callosum of adult wild-type and Bmal1 knockout (Bmal1-/-) mice; mRNA profiles in adult neural stem cells (neurospheres) cultured from the SVZ of wild-type and Bmal1-/- mice
 
Contributor(s) Kim JY
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Submission date Jul 23, 2019
Last update date Aug 01, 2022
Contact name Hao Huang
E-mail(s) haohuang@seu.edu.cn
Organization name Southeast University
Department Department of Bioinformatics
Street address Dongnandaxue Road
City Nanjing
ZIP/Postal code 211189
Country China
 
Platforms (1)
GPL23479 BGISEQ-500 (Mus musculus)
Samples (11)
GSM3966390 WT-NSP-rep1
GSM3966391 WT-NSP-rep2
GSM3966392 WT-NSP-rep3
Relations
BioProject PRJNA556260
SRA SRP216077

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
GSE134748_RAW.tar 2.0 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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