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Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination (RNA-Seq of mouse neural stem cells)

ABSTRACT: To better understand the transcriptome of mouse neural stem cells (including known genes and novel long non coding RNA genes), RNA-Seq was performed on the polyadenylated fraction of RNA isolated from cell samples. Read mapping and transcriptome construction were done by using optimized pipeline which integrate Tophat followed by Cufflinks.

ORGANISM(S): Mus musculus

PROVIDER: GSE74643 | GEO | 2015/11/04

SECONDARY ACCESSION(S): PRJNA301060

REPOSITORIES: GEO

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Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination (RNA-Seq of mouse neural stem cells)

Project description:To better understand the transcriptome of mouse neural stem cells (including known genes and novel long non coding RNA genes), RNA-Seq was performed on the polyadenylated fraction of RNA isolated from cell samples. Read mapping and transcriptome construction were done by using optimized pipeline which integrate Tophat followed by Cufflinks. mRNA profiles of mouse neural stem cells were generated by RNA-sequencing.

2015-11-04 | E-GEOD-74643 | biostudies-arrayexpress

Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination (RNA-Seq of differentiated NSC after lnc-OPC knockdown)

Project description:To quantitative analysis of transcriptome changes caused by lnc-OPC knockdown during OPC differentiation from NSC, lentivirus-based short hairpin RNAs were used to knockdown the lnc-OPC expression in a neural stem cell culture . Subsequently, puromycin-selected NSCs were differentiated to OPC in culture for three days.RNA-Seq was performed on the polyadenylated fraction of RNA isolated from cell samples. DEseq was used for differential gene expression analysis caused by lnc-OPC knockdown. GO functional term enrichment analysis of differential gene expression caused by lnc-OPC knockdown, revealed significant enrichment of ‘oligodendrocyte development’, ‘oligodendrocyte differentiation’, ‘glia cell development’, and ‘axon ensheathment’ terms that are associated with oligodendrogenesis.

2015-11-04 | GSE74647 | GEO

Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination (RNA-Seq of differentiated NSC after lnc-OPC knockdown)

Project description:To quantitative analysis of transcriptome changes caused by lnc-OPC knockdown during OPC differentiation from NSC, lentivirus-based short hairpin RNAs were used to knockdown the lnc-OPC expression in a neural stem cell culture . Subsequently, puromycin-selected NSCs were differentiated to OPC in culture for three days.RNA-Seq was performed on the polyadenylated fraction of RNA isolated from cell samples. DEseq was used for differential gene expression analysis caused by lnc-OPC knockdown. GO functional term enrichment analysis of differential gene expression caused by lnc-OPC knockdown, revealed significant enrichment of âoligodendrocyte developmentâ, âoligodendrocyte differentiationâ, âglia cell developmentâ, and âaxon ensheathmentâ terms that are associated with oligodendrogenesis. mRNA profiles of differentiiated NSC samples after lnc-OPC knockdown by RNA-sequencing.

2015-11-04 | E-GEOD-74647 | biostudies-arrayexpress

Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination.

Project description: Not available

| S-EPMC4980008 | biostudies-literature

Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-11-04 | GSE74648 | GEO

Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-11-04 | E-GEOD-74648 | biostudies-arrayexpress

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Project description:Differential Gene and Transcript Expression Analysis with TopHat and Cufflinks

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Origins and functional evolution of Y chromosome gene repertoires across the class Mammalia

Project description:We collected (Illumina) RNA-seq data (polyadenylated RNA fraction) for a number of tissue samples from common marmoset and elephant. We developed a subtraction approach based on male/female RNA-seq data, Illumina genomic data and available genomes to identify and assemble Y transcripts. For marmoset samples, we added Y coding genes and noncoding sequences to the reference genomes in order to assess their expression levels. We then mapped all RNA-seq reads with TopHat 1.4.0 and used Cufflinks 2.0.0 (all mapped reads, embedded multi-read and fragment bias correction) to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all genes in the genomes with our refined annotations. Sequence and expression levels of reconstructed Y-linked genes

2014-04-15 | E-GEOD-50747 | biostudies-arrayexpress

Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination (OLIG2 Chromatin immunoprecipitation sequencing (ChIP-Seq) in mouse neural stem cells)

Project description:To better understand the OLIG2 binding site in the whole-genome of mouse neural stem cells, ChIP was performed using 107 mouse neural stem cells. The ChIP-Seq library was constructed by using DNA SMART ChIP-Seq Kit according to the manufacturer's instructions (Clontech) and was sequenced on the Illumina HiSeq 2000 Sequencer.

2015-11-04 | GSE74646 | GEO

2015-11-04 | E-GEOD-74646 | biostudies-arrayexpress

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