|
Status |
Public on Oct 24, 2016 |
Title |
Taira201203_XENLA_spleen |
Sample type |
SRA |
|
|
Source name |
spleen
|
Organism |
Xenopus laevis |
Characteristics |
strain: J-strain tissue: spleen 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
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|
|
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.
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|
|
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 |
SAMN04111059 |
SRA |
SRX1286469 |