Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq profiles of WT and Qk-KO corpus callosum and oligodendrocytes

ABSTRACT: RNA-seq profiles of WT and Qk-KO corpus callosum and oligodendrocytes

PROVIDER: PRJNA416936 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6249680_1.fastq.gz	Fastqsanger.gz
	SRR6249680_2.fastq.gz	Fastqsanger.gz
	SRR6249681_1.fastq.gz	Fastqsanger.gz
	SRR6249681_2.fastq.gz	Fastqsanger.gz
	SRR6249672_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

RNA-seq profiles of WT and Qk-KO corpus callosum and oligodendrocytes

Project description:This study is to analyze the transcriptomic profiles of Plp-CreERT2;QKLoxP/LoxP (Qk-KO) and Plp-CreERT2;QKLoxP/+ (WT) mice and WT and Qk-KO oligodendrocytes to determine the differentially expressed genes.

2020-01-04 | GSE106468 | GEO

scRNAseq of Mertk-WT and Mertk-KO corpus callosum

Project description:scRNAseq of Mertk-WT and Mertk-KO corpus callosum

| PRJNA625324 | ENA

Proteome of the Human Corpus Callosum

Project description:Characterization of the human Anterior Temporal Lobe and Corpus Callosum: C-HPP

2014-06-05 | PXD000547 | Pride

Proteome dynamics during postnatal mouse corpus callosum development

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

Bulk RNAseq of AnnexinV+ and AnnexinV- cells from the Mertk-KO corpus callosum at the 4 week cuprizone timepoint

Project description:Purpose: Following 4 weeks of 0.2% cuprizone treatment, Mertk-KO mice accumulate dying cells in the corpus callosum (based on cleaved-cas3 staining). These cells are not seen in Mertk-WT animals at the same cuprizone timepoint. The goal of this study is to identify these dying cells in the Mertk-KO corpus callosum Methods: 2 biological replicates (mice) were used. Corpus callosa were dissected from Mertk-KO mice after 4 weeks of 0.2% cuprizone treatment. Tissues were dissected into single cells using Miltenyi Neural Tissue Dissociation Kit (P) and stained with Annexin V. The stained cell suspensions were then FAC sorted into Annexin V+ and Annexin V- populations. RNA from these cells were extracted using QIAGEN RNeasy kit. Results: Bulk RNA-Seq data were analyzed using an in-house pipeline consisting of GSNAP HTSeqGenie. Reads aligning uniquely to exons were counted to each gene, and size-factor normalization was used to calculating nRPKM statistic. Conclusions: Based on the differences of transcriptomic profiles of AnnexinV+ and AnnexinV- cells, we conclude that the dying AnnexinV+ cells are microglia.

2021-04-13 | GSE148677 | GEO

scRNAseq of Mertk-WT and Mertk-KO corpus callosum

Project description:Purpose: The goal of this study is to characterize the the different CNS cell types in the mouse corpus callosum over three different cuprizone treatment timepoints - (Baseline, 4 weeks, 4 weeks + 3 weeks of recovery) and compare the Mertk-WT vs Mertk-KO response to demyelination. Methods: 3-4 biological replicates (mice) were used for each timepoint/genotype. Tissues were dissociated into single cells for preparation of 10X libraries and sequenced with HiSeq 2500 (Illumina). Results: scRNA-Seq data were analyzed with an in-house analysis pipeline. Briefly, reads were demultiplexed based on perfect matches to expected cell barcodes. Transcript reads were aligned to the mouse reference genome (GRCm38) using GSNAP (Wu and Nacu, 2010). Only uniquely mapping reads were considered for downstream analysis. Transcript counts for a given gene were based on the number of unique molecular identifiers (UMIs) for reads overlapping exons in sense orientation. To account for sequencing or PCR errors, one mismatch was allowed when collapsing UMI sequences. Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Cells with less than 1000 total UMIs were discarded. Conclusions: We show differences between Mertk-WT and Mertk-KO cellular profiles, particularly at the 4 week Cuprizone timepoint. In addition, our data show a distinct, yet heterogenous, population of oligodendrocytes that arise in the cuprizone model where remyelination is spontaneous and robust. Our results provide new insights into the cellular response to demyelination, that includes a resource for comparing and interpreting neurodegenerative disease models.

2021-04-13 | GSE148676 | GEO

RNA-seq profiles of WT and Qk-KO freshly isolated oligodendrocytes

Project description:RNA-seq profiles of WT and Qk-KO freshly isolated oligodendrocytes

| PRJNA516872 | ENA

Proteome of the Human Corpus Callosum

Project description:Characterization of the human Anterior Temporal Lobe and Corpus Callosum: C-HPP

2019-06-10 | MSV000083947 | MassIVE

RNAseq of mouse corpus callosum from WT or TRPA1-KO animals under chronic cerebral hypoperfusion

Project description:Chronic cerebral hypoperfusion is manifested in various CNS diseases accompanied by cognitive impairment, such as dementia, however the precise mechanism of chronic cerebral hypoperfusion-induced cognitive impairment remains unknown. Recently, transient receptor potential ankyrin 1 (TRPA1), activated by oxidative stress, was reported to be involved in the cerebrovascular diseases, therefore we investigated the pathophysiological role of TRPA1 in chronic cerebral hypoperfusion using a mouse bilateral common carotid artery stenosis (BCAS) model. Early cognitive impairment and white matter injury was induced by BCAS in TRPA1-knockout (TRPA1-KO) but not wild-type (WT) mice. For further investigation into the involvement of TRPA1 in chronic cerebral hypoperfusion, we conducted RNA sequence (RNAseq) in the corpus callosum from sham- and BCAS-operated WT and TRPA1-KO mice.

2023-08-08 | GSE201513 | GEO

RNA-Seq of the corpus callosum from 12 individuals

Project description:We performed RNA-Seq for the corpus callosum sampled from 12 individuals. The samples were dissected from the frozen postmortem brain. The 12 individuals were matched by their age, sex and ethnicity for the postmortem brain samples, but differed in their disease status with half of the subjects were diagnosed with autism spectrum disorders.

2014-12-31 | GSE62098 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data