|
| Status |
Public on Jun 04, 2019 |
| Title |
Stage 10 vegetal mass uninjected replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Xenopus tropicalis embryo
|
| Organism |
Xenopus tropicalis |
| Characteristics |
developmental stage: Stage 10.5 (equivalent)
tissue: Vegetal masses
|
| Treatment protocol |
Vegetal masses were dissected at stage 9 and RNA was harvested at stage 10.5
|
| Growth protocol |
Xenopus tropicalis females were injected with 10 units of Chorulon (Merck and Co.) 1-3 nights before embryo collection and 100 units of Chorulon on the day of embryo collection. Eggs were collected in a dish coated with 0.1% BSA in 1/9x MMR. The eggs are in vitro fertilized with sperm suspension in 0.1% BSA in 1/9x MMR. The embryos are dejellied with 3% cysteine in 1/9x MMR, pH 7.8, 10 minutes after fertilization and are then ready for manipulation. Embryos were staged using the Nieukwoop-Faber developmental table.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the acid guanidinium thiocyanate method of Chomczynski and Sacchi (1987: Analytical Biochemistry 162:156-159). Final RNA pellets were resuspended in DEPC-treated water and then precipitated overnight at 4°C in 2.5M LiCl to remove contaminating genomic DNA.
RNA-seq libraries were generated using Smart-seq2 cDNA synthesis followed by tagmentation, quality-tested using an Agilent Bioanalyzer 2100, quantified using KAPA qPCR and sequenced using Illumina sequencers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
processed data file: double-MO-vegt,otx1-readcounts.txt
processed data file: double-MO-vegt,otx1-TPM.txt
|
| Data processing |
RNA-seq gene expression calling: Reads were aligned using RSEM v.1.2.12 (Li and Dewey 2011) and Bowtie v2.2.7 (Langmead and Salzberg 2012) to the Xenopus tropicalis genome version 9.0 (Hellsten et al., 2010; Xenbase FTP). Read counts and transcripts per million were extracted from RSEM results output.
Genome_build: Xenopus tropicalis genome v 9.0
|
| |
|
| Submission date |
Aug 02, 2018 |
| Last update date |
Jun 04, 2019 |
| Contact name |
Kitt D. Paraiso |
| E-mail(s) |
kparaiso@uci.edu
|
| Phone |
949-824-7950
|
| Organization name |
University of California, Irvine
|
| Department |
Department of Developmental and Cell Biology
|
| Lab |
Ken W.Y. Cho
|
| Street address |
4410 Nat Sci II, University of California, Irvine
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL23182 |
| Series (1) |
| GSE118024 |
Endodermal maternal transcription factors establish super enhancers during zygotic genome activation |
|
| Relations |
| BioSample |
SAMN09760049 |
| SRA |
SRX4501222 |
