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Series GSE51572 Query DataSets for GSE51572
Status Public on Oct 24, 2013
Title Sub-Cellular Transcriptomics – Dissection of the mRNA composition in the axonal compartment of sensory neurons
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary RNA localization is a regulatory mechanism that is conserved from bacteria to mammals. Yet, little is known about the mechanism and the logic that govern the distribution of RNA transcripts within the cell. Here we present a novel organ culture system, which enables the isolation of RNA specifically from NGF dependent re-growing peripheral axons of mouse embryo sensory neurons. In combination with massive parallel sequencing technology, we determine the sub-cellular localization of most transcripts in the transcriptome. We found that the axon is enriched in mRNAs that encode secreted proteins, transcription factors and the translation machinery. In contrast, the axon was largely depleted from mRNAs encoding transmembrane proteins, a particularly interesting finding, since many of these gene products are specifically expressed in the tip of the axon at the protein level. Comparison of the mitochondrial mRNAs encoded in the nucleus with those encoded in the mitochondria, uncovered completely different localization pattern, with the latter much enriched in the axon fraction. This discovery is intriguing since the protein products encoded by the nuclear and mitochondrial genome form large co-complexes. Finally, focusing on alternative splice variants that are specific to axonal fractions, we find short sequence motifs that are enriched in the axonal transcriptome. Together our findings shed light on the extensive role of RNA localization and its characteristics.
Overall design For each RNA sample, Spinal Cords\ DRGs were dissected from 40 E13.5 embryos and cultured for 48H. Total RNA was extracted from whole DRG and Peripheral axons. Poly-A enriched. In duplicates, using GAIIx. Read length - 80nt.
Contributor(s) Minis A, Yaron A
Citation(s) 24127433
Submission date Oct 23, 2013
Last update date May 15, 2019
Contact name Avraham Yaron
Phone 972-8-9346241
Organization name Weizmann Institute of Science
Department Department of Biological Chemistry
Lab Yaron Lab
Street address P.O.B 26
City Rehovot
ZIP/Postal code 76100
Country Israel
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (4)
GSM1248600 Dorsal Root Ganglia Rep1
GSM1248601 Dorsal Root Ganglia Rep2
GSM1248602 Peripheral Axons Rep1
BioProject PRJNA223524
SRA SRP031843

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Supplementary file Size Download File type/resource
GSE51572_Cufflinks_Refseq_Merged_transcripts.txt.gz 418.8 Kb (ftp)(http) TXT
GSE51572_Cufflinks_UCSC_Merged_transcripts.txt.gz 1.8 Mb (ftp)(http) TXT
GSE51572_merged_igenome_strict_raw_and_norm.xlsx.gz 2.5 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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