|
| Status |
Public on Oct 24, 2016 |
| Title |
Taira201203_XENLA_eye |
| Sample type |
SRA |
| |
|
| Source name |
eye
|
| Organism |
Xenopus laevis |
| Characteristics |
strain: J-strain
tissue: eye
clutch: Taira
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole tissue was minced before mRNA extraction; mRNA was extracted with TRIzol protocol; the column purification was performed after extraction.
Standard non-strand-specific RNA-seq protocol for HiSeq 2000, with poly-A capturing method
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
TairaUeno_XENLA_tissue.JGIv18pV2_cdna_final.bwa_mem+rsem.indiv_tpm.txt.gz
|
| Data processing |
Mapped paired-reads to primary transcripts with bwa mem (0.7.10)
Filtered out non-compatible hits for RSEM (local alignment, gapped alignment, multi hits, etc)
Calculate TPM with RSEM (1.2.19)
Genome_build: XENLA_JGIv18p (X. laevis JGI gene model version 1.8 primary transcripts)
Supplementary_files_format_and_content: TPMs calculated by RSEM for individual samples. X. laevis has a genome duplication (a pair of large chromosome and small chromosome; see Fig 3 at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3806017/). The consortium decided to call the gene with the suffix (L or S) of the type of chromosome.
|
| |
|
| Submission date |
Sep 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Taejoon Kwon |
| E-mail(s) |
tkwon@unist.ac.kr
|
| Organization name |
Ulsan National Institute of Science and Technology
|
| Department |
Department of Biomedical Engineering
|
| Street address |
50 Unist-gil
|
| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17682 |
| Series (2) |
| GSE73419 |
Tissue gene expression of Xenopus laevis J strain [tissue] |
| GSE73431 |
Developmental gene expression of Xenopus laevis J strain |
|
| Relations |
| BioSample |
SAMN04111049 |
| SRA |
SRX1286459 |
