|
| Status |
Public on Aug 05, 2022 |
| Title |
UIC_13 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Embryo
|
| Organism |
Xenopus tropicalis |
| Characteristics |
treatment: control
time: 13
|
| Treatment protocol |
Embryos were kept at 25ºC either in 1/9X MR or in 10 mM KCl solution, and 10 embryos were harvested per time point and condition every 30 min starting at stage 8 and concluding at stage 13.
|
| Growth protocol |
We induced ovulation, performed IVF, and raised embryos in 1/9xMR, We staged X. tropicalis embryos according to Nieuwkoop and Faber.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples were immediately frozen and kept at -80ºC until homogenized in 100 ml Trizol spiked with ERCC RNA Spike-In Mix. 10 ml ERCC RNA Spike-In Mix (Thermo Fisher Scientific) were first diluted into a final volume of 870 ml DEPC water and then further diluted 1:10 into Trizol, which was used to homogenize the samples. Total RNA was purified from the embryo Trizol homogenates according to the manufacturer’s recommendations. After isopropanol precipitation, RNAs were resuspended in DEPC water and any contaminating genomic DNA was removed by overnight precipitation in 5M LiCl at 4ºC. RNA was subsequently pelleted and washed twice with 70% ethanol. All RNAs were resuspended in DEPC water (2 ml/embryo), and finally, RNA quality was verified by Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Stranded paired end 100bp RNA-seq reads were aligned to the Xt9.1 genome with ERCC spikes using RSEM-STAR pipeline, with additional options "--seed 1618 --calc-pme --calc-ci --estimate-rspd --paired-end". ERCC spikes were used to build a GC-bias dinucleotide correction model applied to all transcripts. Gene level corrected quantifications provided.
Genome_build: Xt9.1
Supplementary_files_format_and_content: Tab delimited file with corrected quantifications for all genes.
|
| |
|
| Submission date |
Oct 27, 2021 |
| Last update date |
Aug 05, 2022 |
| Contact name |
Nick Owens |
| Organization name |
University of Exeter Medical School
|
| Street address |
Barrack Road
|
| City |
Exeter |
| State/province |
Exeter |
| ZIP/Postal code |
EX2 5DW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30018 |
| Series (1) |
| GSE186670 |
Membrane potential drives the exit from pluripotency and the ontogeny of cell fate via calcium and mTOR |
|
| Relations |
| BioSample |
SAMN22601406 |
| SRA |
SRX12798163 |
