|
| Status |
Public on Jul 22, 2016 |
| Title |
Embryo-Stage 6-family 1-WTTS |
| Sample type |
SRA |
| |
|
| Source name |
Embryo_Stage 6_WTTS
|
| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: Embryo
developmental stage: Stage 6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols and standard Ion Torrent protocols. WTTS libraries were prepared based on our protocol. The WTTS method includes several major steps: fragmentation, polyA+ RNA enrichment, 1st strand cDNA synthesis, size selection and PCR amplication.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling .Torrent Suite™ Software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Xenopus tropicalis genome using CLC genomics workbench. The Xenopus tropicalis genome contains both Xenopus tropicalis 7.1 genome annotation and NCBI Xenopus tropicalis refseq.
Genome_build: Xenopus tropicalis v7.1
|
| |
|
| Submission date |
Nov 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhihua Jiang |
| E-mail(s) |
jianglabwsu@gmail.com
|
| Organization name |
Washington State University
|
| Department |
Animal Science
|
| Lab |
Jianglab
|
| Street address |
Veterinary and Biomedical Research Building, Room 151
|
| City |
Pullman |
| State/province |
WA |
| ZIP/Postal code |
99164-7620 |
| Country |
USA |
| |
|
| Platform ID |
GPL21123 |
| Series (1) |
| GSE74919 |
Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline. |
|
| Relations |
| BioSample |
SAMN04260338 |
| SRA |
SRX1427066 |
