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| Status |
Public on May 23, 2022 |
| Title |
Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The goal of this study is to use RNA-seq to investigate the molecular mechanisms by which REST inhibition regulates corticalspinal axon regeneration. To achieve this goal, cortical motor neurons from adult wild-type (WT) and REST conditional knockout (cKO) were purified at 1, 3, 7 days following spinal cord injury (SCI) or sham operation. RNA-seq libraries for cortical motor neurons were prepared with the QuantSeq mRNA-Seq library prep kit FWD for Illumina (Lexogen) and sequenced using HiSeq4000 (Illumina). Sequenced reads were mapped to reference genome (mm10) using STAR, and count level data were quantifed using Salmon. Differential gene expression analysis was performed using limma voom.
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| Overall design |
mRNA profiles were performed in cortical motor neurons from wild-type or REST cKO mice that were recovered 1, 3, 7 days following SCI or sham operation. Each group has 3-4 replicates with ~1000 cells in each replicate.
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| Contributor(s) |
Cheng Y, Geschwind D |
| Citation(s) |
35906210 |
| Submission date |
Dec 06, 2019 |
| Last update date |
Aug 05, 2022 |
| Contact name |
Yuyan Cheng |
| E-mail(s) |
ycheng316@gmail.com
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| Organization name |
UCLA
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| Department |
Neurology
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| Lab |
Daniel Geschwind
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| Street address |
695 Charles E Young Dr S Rm 2305
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (25)
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| GSM4209178 |
Cortical motor neurons, GFP_1 (sample1) |
| GSM4209179 |
Cortical motor neurons, tdTomato_7 (sample2) |
| GSM4209180 |
Cortical motor neurons, GFP_0 (sample3) |
| GSM4209181 |
Cortical motor neurons, GFP_7 (sample4) |
| GSM4209182 |
Cortical motor neurons, GFP_3 (sample5) |
| GSM4209183 |
Cortical motor neurons, tdTomato_0 (sample6) |
| GSM4209185 |
Cortical motor neurons, GFP_7 (sample7) |
| GSM4209187 |
Cortical motor neurons, GFP_1 (sample8) |
| GSM4209188 |
Cortical motor neurons, tdTomato_3 (sample9) |
| GSM4209190 |
Cortical motor neurons, GFP_0 (sample10) |
| GSM4209192 |
Cortical motor neurons, GFP_1 (sample11) |
| GSM4209193 |
Cortical motor neurons, GFP_7 (sample12) |
| GSM4209194 |
Cortical motor neurons, tdTomato_7 (sample13) |
| GSM4209195 |
Cortical motor neurons, GFP_0 (sample14) |
| GSM4209196 |
Cortical motor neurons, tdTomato_3 (sample15) |
| GSM4209197 |
Cortical motor neurons, GFP_3 (sample16) |
| GSM4209198 |
Cortical motor neurons, GFP_0 (sample17) |
| GSM4209199 |
Cortical motor neurons, tdTomato_0 (sample18) |
| GSM4209200 |
Cortical motor neurons, tdTomato_1 (sample19) |
| GSM4209201 |
Cortical motor neurons, tdTomato_3 (sample20) |
| GSM4209202 |
Cortical motor neurons, GFP_3 (sample22) |
| GSM4209203 |
Cortical motor neurons, tdTomato_0 (sample23) |
| GSM4209204 |
Cortical motor neurons, tdTomato_1 (sample25) |
| GSM4209205 |
Cortical motor neurons, tdTomato_7 (sample26) |
| GSM4209206 |
Cortical motor neurons, tdTomato_3 (sample27) |
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| Relations |
| BioProject |
PRJNA594009 |
| SRA |
SRP234983 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE141583_REST_geneInfo.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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