Communication between corpus callosum and SVZ mediated by locally controlled circadian clocks during demyelination
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA556260 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9736910.fastq.gz | Fastqsanger.gz | |||
| SRR9736911.fastq.gz | Fastqsanger.gz | |||
| SRR9736912.fastq.gz | Fastqsanger.gz | |||
| SRR9736913.fastq.gz | Fastqsanger.gz | |||
| SRR9736914.fastq.gz | Fastqsanger.gz |
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Project description: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.
2022-07-31 | GSE134748 | GEO
Project description:To determine expression profiles of cytokines and growth factor profiles in the subventricular zone (SVZ) after demyelination we performed gene array analysis. In SVZ after 4 days post lesin (dpl) LPC-injected tissue, demonstrated regulation of BMP pathway elements, including increased chordin, noggin, and ChorR, and decreased BMP4, compared to NaCl-injected tissue. GEArrayTM expression array systems (cat#OMM031 SuperArray, Bethesda, MD) consisted of spotted cDNA fragments encoding 113 mouse genes for neurotrophic signaling molecules involved in neuronal growth and differentiation, as well as regeneration and survival. Control sequences (PUC18, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), peptidylpropyl isomerase A (Ppia), and ?-actin) were also included. These microarrays were employed to compare SVZ gene expression 4 days after NaCl or LPC injection in corpus callosum. Total RNA was isolated by Trizol (Invitrogen) and processed for microarray hybridization following the manufacturer’s instructions. Arrays were visualized by autoradiography, and hybridization signals were scanned and analyzed for density in GEArray Expression Analysis Suite 2.0. The normalized value for each gene was calculated by dividing the value of each gene by the average value of the housekeeping genes GAPDH, Ppia, and ?-actin.
2010-04-13 | E-GEOD-21310 | biostudies-arrayexpress
Project description:To determine expression profiles of cytokines and growth factor profiles in the subventricular zone (SVZ) after demyelination we performed gene array analysis. In SVZ after 4 days post lesin (dpl) LPC-injected tissue, demonstrated regulation of BMP pathway elements, including increased chordin, noggin, and ChorR, and decreased BMP4, compared to NaCl-injected tissue.
2010-04-13 | GSE21310 | GEO
Project description:Mouse cuprizone (CPZ ) model of experimental de- and remyelination was applied to mimic demyelination pathology of multiple sclerosis. In order to identify differentially expressed microRNAs involved in de- and remyelination, the affected areas of corpus callosum were isolated from mice exposed to CPZ and conducted an Agilent microarray analysis. To induce demyelination, CPZ was administrated for four weeks. Spontaneous remyelination occurs as mice returned to the regular diet after four weeks feeding with CPZ (DEM_4w). Remyelination was examined at two time points: acute remyelination induced by four weeks CPZ feeding followed by two days of regular diet (two days remyelination: REM_2d), and full remyelination induced by four weeks CPZ feeding followed by two weeks of regular diet (two weeks remyelination: REM_2w). Control mice (C) were kept on a normal diet. The following groups representing de- and remyelinisation pathology in corpus callosum of CPZ-treated mice were compared: Demyelination: 4weeks CPZ: DEM_4w; Acute remyelination: 4 weeks CPZ +2 days UNTREATED: REM_2d; Full remyelination: 4 weeks CPZ +2 weeks UNTREATED: REM_2w; and UNTREATED control (C). The experiments were performed using 2-4 animals per groups.
2018-04-11 | GSE100662 | GEO
Project description:Mouse cuprizone (CPZ ) model of experimental de- and remyelination was applied to mimic demyelination pathology of multiple sclerosis. The aim of the study was to profile whole genome expression to identify differentially expressed genes during the demyelinisation and after discontinuation of cuprizon treatment, during rapid remyelinisation in affected areas of mouse corpus callosum. Control mice were kept on a normal diet. The following groups representing de- and remyelinisation pathology in corpus callosum of CPZ-treated mice were compared: Partial demyelination: 2weeks CPZ (dem_2w); Complete demyelination: 4weeks CPZ (dem_4w); Remyelination: 4weeks CPZ + UNTREATED (rem); and UNTREATED control (C). The experiments were performed using 3-4 animals per groups.
2018-09-06 | GSE100663 | GEO
Project description:Corpus callosum bulk RNA sequencing of a cuprizone mouse model of demyelination
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Project description:Characterization of the human Anterior Temporal Lobe and Corpus Callosum: C-HPP
2014-06-05 | PXD000547 | Pride
Project description:CX3CR1-GFP mice were fed with cuprizone for 4 weeks to induce brain demyelination. The central and lateral parts of the corpus callosum (CC) were then separately dissected, dissociated and GFP+ microglial cells were isolated by FACS. 2133 migroglial cells from medial CC and 2304 cells from lateral CC were then processed for single-cell RNA-seq analysis. Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina Nextseq 500.
2021-06-04 | GSE144202 | GEO
Project description:NestinCreERT2:RosaYFP mice were fed with cuprizone for 4 weeks to induce brain demyelination. Corpus callosum was then dissected, dissociated and YFP+ subventricular zone-derived cells were isolated by FACS. 1931 cells were then processed for single-cell RNA-seq analysis. Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina Nextseq 500.
2021-06-04 | GSE144201 | GEO
Project description:Formation of cortical connections requires the precise coordination of several discrete stages. This is particularly significant with regard to the corpus callosum, the largest white matter structure bridging both cerebral hemispheres, whose development undergoes several dynamic stages including the crossing of axon projections, the elimination of exuberant projections, and the myelination of established tracts. To comprehensively characterize the molecular events in this dynamic process, we set to determine the distinct temporal expression of proteins regulating the formation of the corpus callosum and their respective developmental functions. Mass spectrometry-based proteomic profiling was performed on early postnatal mouse corpus callosi, for which limited evidence has been obtained previously, using stable isotope of labeled amino acids in mammals (SILAM). The analyzed corpus callosi had distinct proteomic profiles depending on age, indicating rapid progression of specific molecular events during this period. The proteomic expression profiles were then segregated into five separate protein clusters, each with distinct trajectories relevant to their intended developmental functions. Our analysis both confirms many previously-identified proteins in aspects of corpus callosum development, and identifies new candidates in understudied areas of development including callosal axon refinement. We present a valuable resource for identifying new proteins integral to corpus callosum development that will provide new insights into the development and diseases afflicting this structure.
2017-03-29 | PXD005271 | Pride