|
| Status |
Public on Nov 07, 2014 |
| Title |
st10.5 FoxH1 MO |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus tropicalis |
| Characteristics |
strain: Nigerian
developmental stage: mid-gastrula stage (st10.5)
treatment: 22.5ng Foxh1 MO microinjected at 1-2 cell stage
|
| Treatment protocol |
Embryos were treated with SB431542 (100μM) at 4-cell stage until stage 10.5 or microinjected with Foxh1 MO (22.5ng) at 1-2 cell stage and cultured until stage 10.5
|
| Growth protocol |
Embryos were cultured in 1/9X MMR at 25°C until the indicated stage.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were extracted from ~25-30 control and experimental early gastrula embryos using the acid guanidinium thiocyanate phenol chloroform method (Chomczynski and Sacchi 1987), followed by selective precipitation of RNA using 2.5M LiCl.
Libraries were prepared using illumina TruSeq™ RNA Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
processed data file: st10.5_Foxh1_MO_gene_exp_diff.txt
|
| Data processing |
Raw RNA-seq reads from Illumina sequencing were mapped to the most recent Xenopus tropicalis genome assemblyusing TopHat (v. 1.3.3) (Trapnell et al. 2009), with a parameter “-G <Xentr7_2_Stable.gff3>”.
The differential expression of genes in control versus perturbed samples were calculated using Cuffdiff (v. 1.3.0) (Roberts et al. 2011) with default settings.
Genome_build: Xenopus tropicalis genome build v 7.1
Supplementary_files_format_and_content: tab-delimited text file containing FPKM values of all annotated gene models and the fold change of each gene in perturbed versus control embryos
|
| |
|
| Submission date |
Dec 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
William Chiu |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, Irvine
|
| Department |
Developmental and Cell Biology
|
| Lab |
Cho
|
| Street address |
Room 4410 Natural Sciences II
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL13741 |
| Series (2) |
| GSE53653 |
Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [RNA-seq] |
| GSE53654 |
Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program |
|
| Relations |
| BioSample |
SAMN02486399 |
| SRA |
SRX399455 |
