|
| Status |
Public on Jan 26, 2023 |
| Title |
TELS S16 embryos hybrid RNA-seq__rep2 |
| Sample type |
SRA |
| |
|
| Source name |
xenopus tropicalis (sperm) X xenopus laevis (egg) hybrids embryo: S16
|
| Organism |
Xenopus tropicalis x Xenopus laevis |
| Characteristics |
tissue: embryo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ovulation and cross-fertilization were carried out according to the protocol described previously with some modification (Gibeaux., 2018). Briefly, Female Xenopus laevis were injected with 500 U HCG. After 12 hours, male Xenopus tropicalis were injected with 150 U HCG. After 2 hours, X. laevis females were squeezed gently to deposit eggs onto clean 9 cm Petri dishes and two X. tropicalis testes collected in 0.5 ml 1xMBS and homogenized using razor blades. Any liquid in the Petri dishes was removed and the per dish eggs were fertilized with mix solution containing 0.1 ml of sperm and 0.9 ml H2O. Eggs were swirled in the solution to individualize eggs as much as possible and incubated for 10 min. Jelly coats were removed with a 2% cysteine solution (add NaOH adjust the pH to 7.8-8.0). After extensive washing (at least four times) with 0.1xMBS, embryos were incubated at 23 °C.
Total RNA was isolated from hybrid embryos using the TransZol Up Plus RNA Kit (Transgen, ER501-01). Libraries were prepared with a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L) according to the manufacturer's instructions. The libraries were sequenced on an Illumina HiSeq 2500 platform, and 150-base paired-end reads were produced. Two biological replicates were generated for control and dark-treated seedlings.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw fastq RNA-seq reads and adapter sequences were removed by Trimmomatic v0.38. Clean reads were mapped to the combined X.tropicalis v10.0 and X.laevis v9.2 reference genome using STAR v2.7.9a
Genome_build: xv10_xl9
Supplementary_files_format_and_content: gene abundance
|
| |
|
| Submission date |
Mar 03, 2022 |
| Last update date |
Jan 26, 2023 |
| Contact name |
Chuihui Hou |
| E-mail(s) |
houch@sustech.edu.cn
|
| Organization name |
Southern University of Science and Technology
|
| Street address |
Xueyuan Avenue
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
| |
|
| Platform ID |
GPL32016 |
| Series (2) |
| GSE197874 |
Super-sized clustered loops anchored at transposon Helitrons in Xenopus tropicalis sperm associate with late gene expression during embryogenesis [RNA-Seq] |
| GSE197877 |
Super-sized clustered loops anchored at transposon Helitrons in Xenopus tropicalis sperm associate with late gene expression during embryogenesis |
|
| Relations |
| BioSample |
SAMN26419826 |
| SRA |
SRX14360688 |
