|
| Status |
Public on Dec 01, 2021 |
| Title |
shControl_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Dorsal Root Ganglia_shControl
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
developmental stage: Embryonic day 13
tissue: Dorsal Root Ganglia
knockdown: shControl
|
| Treatment protocol |
Cells were either treated with shUHRF1 or shControl lentivirus as described
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Invitrogen PureLink RNA Minikit with on-column Dnase treatment
Ribo-Zero Gold rRNA depletion then Clontech SMARTer cDNA Synthesis kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adapter ends were trimmed using FastQC
Reads were aligned to mm10 using STAR-align with default settings
Reads aligned to genes were counted using Htseq-counts with default settings
Differential expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Text files include gene counts; XLSX File includes differential expression analysis from DESeq2
|
| |
|
| Submission date |
Nov 23, 2016 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Valeria Cavalli |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University in St. Louis
|
| Department |
Anatomy and Neurobiology
|
| Street address |
660 S. Euclid Ave.
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE90476 |
miRNA-9 regulates axon regeneration through the transcriptional regulator REST and the epigenetic factor UHRF1 [RNA-seq] |
| GSE90477 |
Gene repression by DNA methylation promotes axon regeneration |
|
| Relations |
| BioSample |
SAMN06051254 |
| SRA |
SRX2371085 |
