|
| Status |
Public on Jul 10, 2018 |
| Title |
SRV-0043 |
| Sample type |
SRA |
| |
|
| Source name |
mid-zeugopod whole tissue
|
| Organism |
Ambystoma mexicanum |
| Characteristics |
tissue: mid-zeugopod
time post amputation (hpa): 0
size of tissue collection: 1mm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mid-zeugopod amputations were conducted on all animals. Exactly 1mm distal most tissue was collected immediately after amputation (0hpa) and 24 hpa. Whole RNA tissue was extracted using the TruSeq RNA library prep kit from Illumina.
HudsonAlpha Institute for Biotechnology generated the RNA-Seq data by preparing cDNA libraries and sequencing approximately 50,000,000 100 bp read pairs per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RSEM processed, expected count values, found in column 4 of processed data file
AMEX_RNASEQ_EXPCOUNT.txt
|
| Data processing |
De novo assembly of RNA-Seq isotigs was accomplished using Trinity’s three-stage protocol (Inchworm, Chrysalis, and Butterfly).
RSEM was used for count estimation with default parameters
Expected counts were extracted in a matrix file format from the RSEM output.
|
| |
|
| Submission date |
Jul 09, 2018 |
| Last update date |
Jul 27, 2018 |
| Contact name |
Varun Bhamidipati Dwaraka |
| E-mail(s) |
varun.dwaraka@uky.edu
|
| Organization name |
University of Kentucky
|
| Department |
Spinal Cord and Brain Injury Research Center
|
| Lab |
Voss Lab
|
| Street address |
741 South Limestone St.
|
| City |
Lexington |
| State/province |
Kentucky |
| ZIP/Postal code |
40536-0509 |
| Country |
USA |
| |
|
| Platform ID |
GPL21473 |
| Series (2) |
| GSE116777 |
Comparative Transcriptomics of Limb Regeneration: Identification of Conserved Expression Changes Among Three Species of Ambystoma [RNA-Seq] |
| GSE116788 |
Comparative Transcriptomics of Limb Regeneration in Ambystoma salamanders |
|
| Relations |
| BioSample |
SAMN09631088 |
| SRA |
SRX4368791 |
