|
| Status |
Public on Nov 10, 2021 |
| Title |
X1To |
| Sample type |
SRA |
| |
|
| Source name |
24h - transection - TORIN1
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: Caudal section of spinal cord
Stage: NF stage 50
surgery: transection
time of isolation after surgery (hours): 24
treatment: Incubated in TORIN1 during first 24 hours after transection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spinal cords from animals at R-stage were dissected in time-series after surgery and immediately stored in RNAlater. Posterioly the purification of total RNA was performed using the RNeasy Mini Kit.
RNA libraries were prepared by TruSeq RNA Library Prep Kit v2. Posterioly these were sequenced on the Illumina HiSeq 2000 and HiSeq 4000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava 1.7 software was used for basecalling.
Paired-end reads were mapped to Xenopus laevis model transcriptome v9.1 (Xenbase) using Bowtie. Gene expression level was quantified by RSEM.
|
| |
|
| Submission date |
Jan 22, 2021 |
| Last update date |
Nov 10, 2021 |
| Contact name |
Juan Larraín |
| E-mail(s) |
jlarrain@bio.puc.cl
|
| Organization name |
Pontificia Universidad Catolica de Chile
|
| Department |
Cellular and Molecular Biology
|
| Lab |
Developmental and Regenerative Biology
|
| Street address |
Portugal 49
|
| City |
Santiago |
| ZIP/Postal code |
8330025 |
| Country |
Chile |
| |
|
| Platform ID |
GPL22393 |
| Series (1) |
| GSE165343 |
High expression profiling analysis of the early response to spinal cord injury identified a key role for mTORC1 signaling |
|
| Relations |
| BioSample |
SAMN17496996 |
| SRA |
SRX9921067 |
