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| Status |
Public on Oct 01, 2018 |
| Title |
Regulation of neuroregeneration by long noncoding RNAs [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In mammals, neurons in the peripheral nervous system (PNS) have regenerative capacity following injury, a capacity which but it is generally absent in the central nervous system (CNS). This difference is attributed, at least in part, to the intrinsic ability of PNS neurons to activate a unique regenerative transcriptional program following injury. Long noncoding RNA (lncRNA) transcripts are typically expressed in a small subset of cell types and may facilitate specificity in regulatory programs. Here we profiled gene expression following sciatic nerve crush in mice, and identified lncRNAs that act in the regenerating neurons, and which are typically not expressed in other contexts. We show that two of these lncRNAs regulate the extent of neuronal outgrowth. We then focus on one of these, Silc1, and show that it regulates neuroregeneration in cultured cells and in vivo, through cis-acting activation of the transcription factor Sox11.
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| Overall design |
RNA-seq of intact DRG, cultured DRG neurons, and adult brain
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| Contributor(s) |
Ulitsky I, Ben-Tov Perry R |
| Citation(s) |
30401432 |
| Submission date |
Mar 06, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Igor Ulitsky |
| E-mail(s) |
igor.ulitsky@weizmann.ac.il
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| Organization name |
Weizmann Institute of Science
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| Street address |
Hertzl St.
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| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (63)
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| GSM3032314 |
DRG 1 day after sciatic nerve injury, rep1 |
| GSM3032315 |
DRG 1 day after sciatic nerve injury, rep2 |
| GSM3032316 |
DRG 1 day after sham operation, rep1 |
| GSM3032317 |
DRG 1 day after sham operation, rep2 |
| GSM3032318 |
DRG 1 day after sham operation, rep3 |
| GSM3032319 |
DRG 4 days after sciatic nerve injury, rep1 |
| GSM3032320 |
DRG 4 days after sciatic nerve injury, rep2 |
| GSM3032321 |
DRG 4 days after sciatic nerve injury, rep3 |
| GSM3032322 |
DRG 4 days after sham operation, rep1 |
| GSM3032323 |
DRG 4 days after sham operation, rep3 |
| GSM3032324 |
DRG 7 days after sciatic nerve injury, rep1 |
| GSM3032325 |
DRG 7 days after sciatic nerve injury, rep2 |
| GSM3032326 |
DRG 7 days after sciatic nerve injury, rep3 |
| GSM3032327 |
DRG 7 days after sham operation, rep1 |
| GSM3032328 |
DRG 7 days after sham operation, rep2 |
| GSM3032329 |
DRG 7 days after sham operation, rep3 |
| GSM3032330 |
Control siRNA, rep1 |
| GSM3032331 |
Control siRNA, rep2 |
| GSM3032332 |
Control siRNA, rep3 |
| GSM3032333 |
Sox11 siRNA, rep1 |
| GSM3032334 |
Atf3 siRNA, rep1 |
| GSM3032335 |
Silc1 siRNA, rep1 |
| GSM3032336 |
Silc1 siRNA, rep2 |
| GSM3032337 |
Norris1 siRNA, rep1 |
| GSM3032338 |
Norris1 siRNA, rep3 |
| GSM3032339 |
WT brain 1 |
| GSM3032340 |
WT brain 2 |
| GSM3032341 |
WT brain 3 |
| GSM3032342 |
WT brain 4 |
| GSM3032343 |
WT brain 5 |
| GSM3032344 |
Silc1 KO brain 1 |
| GSM3032345 |
Silc1 KO brain 2 |
| GSM3032346 |
Silc1 KO brain 3 |
| GSM3032347 |
Silc1 KO brain 4 |
| GSM3032348 |
Silc1 KO brain 5 |
| GSM3032349 |
DRG WT injury day 4 1 |
| GSM3032350 |
DRG WT injury day 4 2 |
| GSM3032351 |
DRG WT injury day 4 3 |
| GSM3032352 |
DRG WT injury day 4 5 |
| GSM3032353 |
DRG WT sham day 4 2 |
| GSM3032354 |
DRG WT sham day 4 3 |
| GSM3032355 |
DRG WT sham day 4 5 |
| GSM3032356 |
DRG Silc1 KO injury day 4 1 |
| GSM3032357 |
DRG Silc1 KO injury day 4 2 |
| GSM3032358 |
DRG Silc1 KO injury day 4 3 |
| GSM3032359 |
DRG Silc1 KO injury day 4 4 |
| GSM3032360 |
DRG Silc1 KO injury day 4 5 |
| GSM3032361 |
DRG Silc1 KO sham day 4 1 |
| GSM3032362 |
DRG Silc1 KO sham day 4 2 |
| GSM3032363 |
DRG Silc1 KO sham day 4 3 |
| GSM3032364 |
DRG Silc1 KO sham day 4 4 |
| GSM3032365 |
DRG Silc1 KO sham day 4 5 |
| GSM3032366 |
DRG WT injury day 7 1 |
| GSM3032367 |
DRG WT injury day 7 2 |
| GSM3032368 |
DRG WT sham day 7 1 |
| GSM3032369 |
DRG WT sham day 7 2 |
| GSM3032370 |
DRG Silc1 KO injury day 7 1 |
| GSM3032371 |
DRG Silc1 KO injury day 7 2 |
| GSM3032372 |
DRG Silc1 KO sham day 7 1 |
| GSM3032373 |
DRG Silc1 KO sham day 7 2 |
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| This SubSeries is part of SuperSeries: |
| GSE119491 |
Regulation of neuroregeneration by long noncoding RNAs |
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| Relations |
| BioProject |
PRJNA437167 |
| SRA |
SRP134051 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE111497_RAW.tar |
6.6 Gb |
(http)(custom) |
TAR (of BW, TXT) |
| GSE111497_stringtie_merge_v1.gtf.gz |
7.9 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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