|
| Status |
Public on Sep 30, 2017 |
| Title |
LIB014416_TRA00035337 |
| Sample type |
SRA |
| |
|
| Source name |
Limb stump
|
| Organism |
Ambystoma mexicanum |
| Characteristics |
condition: Control
tissue: Limb stump
genotype: wild-type
strain: leucistic
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. The Illumina TruSeq v2 protocol was used to generate barcoded sequencing libraries. Paired-end, 50bp sequencing was performed on the Illumina HiSeq 2500 at Harvard Medical School's Biopolymers facility.
RNA libraries were prepared for sequencing using the Illumina TruSeq v2 protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calls were performed using Illumina CASAVA 1.8.2
Trinity was used for de novo transcriptome assembly performed by Stirplate.
Counts of RNA-seq fragments mapping to transcripts in our assembly were determined for each tissue type using RSEM .
Genome_build: n/a currently for axoltol
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and TMM-normalized FPKMs for each Sample
Supplementary_files_format_and_content: Trinity_transcripts.counts.matrix: abundance measurements (fragment counts)
Supplementary_files_format_and_content: Trinity_transcripts.TMM.fpkm.matrix: abundance measurements (FPKM)
|
| |
|
| Submission date |
Aug 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jessica Whited |
| Organization name |
Brigham and Women's Hospital
|
| Street address |
60 Fenwood Road
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL22800 |
| Series (1) |
| GSE103087 |
Identification of regenerative roadblocks via repeat deployment of limb regeneration in axolotls |
|
| Relations |
| BioSample |
SAMN07559533 |
| SRA |
SRX3131574 |
