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| Status |
Public on Feb 26, 2019 |
| Title |
Transcriptome analysis of mouse cortical development and characterization of long non-coding RNAs |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Cortical neural progenitor cells (NPCs) change their competency over time during development, giving rise to distinct cell types sequentially. Many genes that govern cortical development are now known, but it remains elusive how their temporal expression is controlled. Recently, long non-coding RNAs are found to be essential for cell-fate specification and precise gene regulation in many developmental events. In this study, strand-specific RNA sequencing studies unveil large amount of long non-coding RNAs are actively and differentially expressed across mouse cortical development. Integration of RNA sequencing data from key stages of developing mouse cortex enables us to cluster coding and non-coding transcripts into co-expression “modules” to infer functional relationships. Intriguingly, the cortical transcriptome undergoes significant changes in early mouse neurogenesis. Cortical long non-coding RNAs tends to be transcribed from genomic loci adjacent to protein-coding genes related to neural development. Finally, we found large amount of predicted enhancer regions are able to transcribe RNAs. This study will help us better understand molecularly how cortical NPCs specify their fates during development, especially roles of lncRNAs in this process.
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| Overall design |
Ribosomal-depletion RNA profiles of dorsal forebrain (cortex) tissues from E10.5 and E12.5 mouse embryos were generated using Illumina HiSeq 2000 and totally 410 million paired-end reads were generated.
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| Contributor(s) |
Li W, Tian K, Mu L, Luo Z, Shen W, Liu J, Zhong X, Li Y, Sheng K, Liu Y, Zhou Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tian Kuan |
| Organization name |
College of Life Sciences at Wuhan University
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| Street address |
Luojiashan
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA240203 |
| SRA |
SRP039434 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE55600_RAW.tar |
570.2 Mb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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