|
| Status |
Public on May 29, 2018 |
| Title |
10 weeks post-pyramidotomy, intramuscular AAV-1 prepro-neurotrophin-3 (5) mRNA |
| Sample type |
SRA |
| |
|
| Source name |
C6-8 dorsal root ganglion
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: dorsal root ganglion
timepoint post-injury: 10 weeks
treatment: AAV1 prepro-neurotrophin-3
strain: lister hooded rats
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA for RNA sequencing was extracted from C6-C8 DRGs from the rats from the pyramidotomy study. Tissue was homogenized in QIAZOL (Qiagen, 79306) and nucleic acids were separated in Phase Locked Gel columns (5Prime, 230 2830). 1.5 volume of 100% ethanol was added to the aqueous phase and transferred to filtered spin columns from the RNA extraction kit (miRNeasy kit, Qiagen, 217004) and we proceeded according to manufacturer's instructions. Samples were also DNase I treated with double volume of the recommended amount (Qiagen, 79254). We estimated the total RNA quality and quantity by spectrophotometry (NanoDrop, ND-1000) and measured the RIN scores (Agilent RNA 6000 Nano Reagents Part I and Agilent 2100 Bioanalyzer). The integrity number for each sample was greater than 7.6, with an average of 8.
The samples were subjected to poly-A enrichment with oligo-dT beads (Illumina) and the library was prepared using the TruSeq Stranded prep kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 17
|
| Data processing |
Basecalling was performed with Illumina's bcl2fastq v1.8.4
Read quality and potential sequencing biases were assessed using custom scripts for quality control of the raw sequencing data
The 50bp paired-end reads were aligned to the reference genome (Rattus Norvegicus rn6) using TopHat2 with default parameters (except for setting mate-inner-dist=100 and mate-std-dev=50
Duplicate reads were identified using picard tools MarkDuplicates and the highest quality read at each position was retained
Reads mapping to each gene feature were counted using htseq-count to create a raw gene count table (RefSeq annotations)
Genome_build: Rnor_6.0 for mRNA
Supplementary_files_format_and_content: text file: raw count matrix table for all sample combined
|
| |
|
| Submission date |
Jun 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Claudia Kathe |
| E-mail(s) |
claudia.kathe@epfl.ch
|
| Organization name |
EPFL
|
| Department |
Center for Neuroprosthetics
|
| Lab |
Courtine Lab
|
| Street address |
Chemin des MInes 9
|
| City |
Geneva |
| ZIP/Postal code |
1202 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE82195 |
Changes in mRNA in the dorsal root ganglion after CNS injury and intramuscular neurotrophin-3 treatment |
| GSE82197 |
Changes in mRNA and small RNA in the dorsal root ganglion after CNS injury and intramuscular neurotrophin-3 treatment |
|
| Relations |
| BioSample |
SAMN05199528 |
| SRA |
SRX1817537 |
