 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 26, 2018 |
| Title |
Bolitoglossa ramosi differential expressed genes during limb regeneration |
| Organism |
Bolitoglossa ramosi |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. To gain broader perspective on the molecular basis of limb regeneration and enhance the molecular toolkit of an emerging plethodontid salamander (Bolitoglossa ramosi), we used RNA-seq to generate transcript sequence data and identify 602 genes that are differentially expressed during limb regeneration. This list was further processed to identify a core set of genes that exhibit conserved expression changes between B. ramosi and the Mexican axolotl (Ambystoma mexicanum), and presumably their common ancestor approximately 180 million years ago. Our study highlights the importance of developing comparative gene expression data for studies of limb regeneration among salamanders.
All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015.
|
| |
|
| Overall design |
To assembly the reference transcriptome, we sequenced individual samples which had pools of different adult animals we did pools of different animals to get the tissues of controls (three biological replicates, n = 9 animals), gut (one biological replicate, n = 1 animal), skin (one biological replicate, n = 1 animal), blastema 20 dpa (one biological, replicate n = 1 animal), blastema 40 dpa (one biological replicate, n = 2 animals), blastema 60 dpa (two biological replicates, n = 5 animals) and 70 dpa (one biological replicate, n = 3 animals).
All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015, which was delivered by the Ministerio del Medio Ambiente (Ministry of Environment) of Colombia to the Principal Investigator.
|
| |
|
| Contributor(s) |
Arenas CM, Woodcock R, Smith J, Voss RS, Delgado JP |
| Citation(s) |
30253734, 32123704 |
| |
| Submission date |
Oct 19, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Jean Paul Delgado |
| E-mail(s) |
jean.delgado@udea.edu.co
|
| Organization name |
University of Atioquia
|
| Department |
Biology
|
| Lab |
Genética, Regeneración y Cáncer
|
| Street address |
Calle 62 # 52-59
|
| City |
medellin |
| State/province |
antioquia |
| ZIP/Postal code |
00000 |
| Country |
Colombia |
| |
|
| Platforms (1) |
| GPL24157 |
Illumina HiSeq 2000 (Bolitoglossa ramosi) |
|
| Samples (10)
|
|
| Relations |
| BioProject |
PRJNA415057 |
| SRA |
SRP120553 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE105232_BoliREF.fa.gz |
105.6 Mb |
(ftp)(http) |
FA |
| GSE105232_EBseq_mean_count_value_log2FC.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
| GSE105232_RAW.tar |
53.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...