|
| Status |
Public on Dec 12, 2013 |
| Title |
Ctrl_1 |
| Sample type |
SRA |
| |
|
| Source name |
Wild-type animal cap, total poly-(A) RNAs
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: Animal cap
phenotype: wild-type
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA isolated from 100 animal caps from X. laevis (stage 20)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Wild-type animal cap, total poly-(A) RNAs, rep 1
|
| Data processing |
Filter out all reads with no-call (‘N’) and low complexity (reads without all 4 bases).
Take reads that both paired-end reads are passed the above condition.
Map to constructed X. laevis gene model (‘Oktoberfest’ version; longest transcript per gene loci) with bowtie1, then calculate RPKM (read counts per kb per 1 million of reads), Calculate FDR with edgeR.
genome_build: X. laevis draft genome (JGI v6.0), X. laevis gene model (Oktoberfest)
supplementary_files_format_and_content: Tab-delimited text file includes RPKM values, fold-change and FDR
|
| |
|
| Submission date |
Sep 04, 2013 |
| 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 (1) |
| GSE50593 |
Coordinated genomic control of ciliogenesis and cell movement by Rfx2 |
|
| Relations |
| BioSample |
SAMN02344710 |
| SRA |
SRX345032 |
