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| Status |
Public on Jun 07, 2011 |
| Title |
Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Mammalian development is an intricate process regulated by multiple gene isoforms and their epigenetic states, which are yet undefined. Using integrative massive parallel sequencing and bioinformatics approach, we built genome-wide inventory of transcript variants, their promoters and histone modification states during normal development, using mouse cerebellum as model system. The data we integrated consists of 29,589 (4,792 novel) promoters that transcribe 61,525 (12,796 novel) distinct mRNAs, corresponding to 14,508 protein-coding and 9,862 non-coding genes. While 68% of the multi-transcript genes exhibit alternative splicing, 78% use alternative transcriptional events that are regulated during cerebellar development through H3K4me3 and H3K27me3. The data presented highlight the magnitude of alternative promoters and transcriptional termination as major source of transcriptome diversity along with alternative splicing. We also show that alternative promoters differentially activated during normal cerebellar development are aberrantly used in medulloblastoma, emphasizing the importance of studying gene regulation and function at the isoform-level.
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| Overall design |
Study of transcriptome diversity in cerebellar development.
We performed mRNA-seq and ChIP-seq experiments. mRNA-seq were performed on total RNA isolated from two P0, P5, P15 and adult cerebellum using 10 microgram of total RNA as the starting material for sequencing library prep. For each stage, mRNA-seq data was obtained from two lanes of a flowcell. For ChIP-seq experiments, solubilized chromatin was prepared by pooling multiple cerebellum tissues (3-18) and then ChIP-enriched DNA (using anti-RNAP II, anti-H3K4me3, anti-H3K27me3, or negative control IgG antibodies) were isolated. 10 microgram of ChIP-enriched DNA was used to prepare the ChIP-seq library for sequencing in a single lane.
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| Contributor(s) |
Pal S, Gupta R, Kim H, Wickramasinghe P, Baubet V, Showe LC, Dahmane N, Davuluri RV |
| Citation(s) |
21712398 |
| Submission date |
Aug 09, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Ravi Gupta |
| E-mail(s) |
rgupta@wistar.org
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| Phone |
215-495-6837
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| Fax |
215-495-6847
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| Organization name |
The Wistar Institute
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| Department |
Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program
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| Lab |
Davuluri Lab
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| Street address |
3601 Spruce Street
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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| Samples (20)
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| Relations |
| SRA |
SRP003462 |
| BioProject |
PRJNA131779 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE23525_RAW.tar |
7.3 Gb |
(http)(custom) |
TAR (of SAM, TXT, WIG) |
| GSE23525_readme.txt |
475 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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