|
| Status |
Public on Aug 07, 2020 |
| Title |
BS-12-3wk-Tadpole-Transected-3 |
| Sample type |
SRA |
| |
|
| Source name |
Hindbrain
|
| Organism |
Xenopus laevis |
| Characteristics |
strain: albino, Xenopus Express
age: stage 53 tadpole
Sex: not determined
|
| Treatment protocol |
Unilateral orbital optic nerve crushes (Zhao and Szaro 1994, doi: 10.1002/cne.903430112) and complete spinal cord transections (Gibbs and Szaro 2018, doi: 10.1101/pdb.prot101030) were performed on fully anesthetized animals (MS222).
|
| Growth protocol |
All animals used in this study were purchased from Xenopus Express, Inc (Brooksville, FL). Prior to surgery, they were acclimated to the lab for at least one week, under a 12L:12D photoperiod, in tanks of condition water at 22C, and fed every other day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Eyes for optic nerve crush studies were rapidly dissected and then homogenized immediately, pooling six eyes for each biological replicate. Because dissections of hindbrain required more time, each hindbrain was placed in 1 mL of RNAlater at room temperature over-night. RNAlater was then aspirated and five pooled hindbrains homogenized for each biological replicate. Total RNA was isolated using the RNA/DNA/Protein Purification kit from Norgen Biotek Corp. with DNase I treatment, following manufactuer's protocols.
Total RNA was enriched for mRNA by ribosomal RNA depletion, which was then used to prepare cDNA libraries using Illumina's TruSeq Stranded Total RNA LT Sample Prep Kit (A&B), with Ribo-Zero Gold.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
5 tadpoles, 3 weeks after spinal cord transection
|
| Data processing |
Read alignments were performed against Xenopus laevis gemome (Xenbase v9.1) using Bowtie2 (V2.2.9) and TopHat (v2.1.1), and annotated using the Mayball gene model.
Differential expression and associated analysis were carried out using Cufflinks/Cuffdiff2 (v2.2.1; per condition dispersion with a min. count of 10) and CummRbund (v2.16.0).
Genome_build: Xenopus laevis Xenbase v9.1
Supplementary_files_format_and_content: text files; FPKM read counts for each transcript
|
| |
|
| Submission date |
Sep 23, 2019 |
| Last update date |
Aug 07, 2020 |
| Contact name |
Ben Gregory Szaro |
| E-mail(s) |
bszaro@albany.edu
|
| Phone |
518-591-8852
|
| Organization name |
University at Albany, State University of New York
|
| Department |
Biological Sciences
|
| Lab |
Life Sciences Research 1059
|
| Street address |
1400 Washington Avenue
|
| City |
Albany |
| State/province |
NY |
| ZIP/Postal code |
12222 |
| Country |
USA |
| |
|
| Platform ID |
GPL21248 |
| Series (1) |
| GSE137844 |
Comparative Gene Expression Profiling between Xenopus Optic Nerve and Spinal Cord Injury to Identify Genes Involved in Successful Regeneration of Vertebrate CNS Axons |
|
| Relations |
| BioSample |
SAMN12819376 |
| SRA |
SRX6888572 |
