|
| Status |
Public on Dec 19, 2018 |
| Title |
Kwon201408_XenopusHybrid_TELS1 |
| Sample type |
SRA |
| |
|
| Source name |
9 hpf whole embryo
|
| Organism |
Xenopus tropicalis x Xenopus laevis |
| Characteristics |
developmental stage: 9 hpf
|
| Growth protocol |
Embryos at 9 hpf were collected
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
To isolate RNA, embryos at stage 9 were homogenized mechanically in TRIzol® (Thermo Fisher Scientific, Waltham, MA) using up to a 30-gauge needle and processed according to manufacturer instructions. After resuspension in nuclease-free H2O, RNAs were cleaned using a RNeasy kit (Qiagen Inc.) according to manufacturer instructions.
Libraries were prepared using manufacturer’s non-standard specific RNA-seq library protocol with poly-A capturing mRNA enrichment method (Illumina, CA, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Xenopus laevis (sperm) x Xenopus tropicalis (egg) hybrid
TELS1
|
| Data processing |
Mapped paired-reads to primary transcripts with bwa mem (0.7.10)
Filtered out reads mapped on multiple targets (i.e. reads mapped on both species)
Genome_build: Xenopus transcripts UTA2014 version (uploaded to GEO)
Supplementary_files_format_and_content: indiv_tpm.txt.gz - TPM for each samples
Supplementary_files_format_and_content: fa.gz - transcripts FASTA file
|
| |
|
| Submission date |
Aug 09, 2018 |
| Last update date |
Dec 19, 2018 |
| 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 |
GPL22797 |
| Series (1) |
| GSE118382 |
Xenopus hybrids provide insight into cell and organism size control |
|
| Relations |
| BioSample |
SAMN09788951 |
| SRA |
SRX4525913 |
