|
| Status |
Public on Oct 29, 2020 |
| Title |
Holothuria glaberrima: Normal mesentery_Normal1 |
| Sample type |
SRA |
| |
|
| Source name |
mesentery
|
| Organism |
Holothuria glaberrima |
| Characteristics |
regenerative stage: Non-regenerating
tissue: mesentery
|
| Treatment protocol |
Organisms were treated with KCl to induce the expelling of their internal organs for the regenerative process to start.
|
| Growth protocol |
Organisms were kept in fish tanks with aerators.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Combination of the method established by Chomczynski (1993) using Tri-reagent® (N.93289, Sigma, USA) and the RNAeasy mini kit (Qiagen, Germany).
TruSeq Stranded mRNA Library Prep Kit (Illumina, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DispersionEstimatesNormal
Normal1
|
| Data processing |
Preprocessing steps of quality, trimming and filtering were done using FastQCv0.11.577 and Trimmomaticv0.3678 (ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDING-WINDOW:4:15 MINLEN:36)
Kmer trimming and digital normalization was applied previously to the assembly process using the khmer package.
A de novo transcriptome assembly was carried out using Trinity
Supplementary_files_format_and_content: Final dispersion estimates obtained with DESeq2 and expression tables with Log2FC of annotated genes for the comparisons.
|
| |
|
| Submission date |
Oct 28, 2020 |
| Last update date |
Oct 29, 2020 |
| Contact name |
David J Quispe |
| E-mail(s) |
[email protected]
|
| Phone |
9392596452
|
| Organization name |
Universty of Puerto Rico
|
| Department |
Biology
|
| Lab |
Developmental Neurobiology Laboratory
|
| Street address |
14, 2534 Av. Universidad Ste. 1401
|
| City |
San juan |
| State/province |
PR |
| ZIP/Postal code |
00925 |
| Country |
Puerto Rico |
| |
|
| Platform ID |
GPL29317 |
| Series (1) |
| GSE160340 |
Transcriptomic Analysis of Early Stages of Intestinal Regeneration in Holothuria glaberrima |
|
| Relations |
| BioSample |
SAMN15960516 |
| SRA |
SRX9052880 |
