|
| Status |
Public on Sep 17, 2014 |
| Title |
Tropicalis_3seq_stage9-Nodal-Inhibited-R1 |
| Sample type |
SRA |
| |
|
| Source name |
mRNA
|
| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: whole embryo
genotype/variation: wild type
treatment: SB treated nodal inhibited
developmental stage: 9
chip antibody: none
|
| Treatment protocol |
For Nodal inhibition, embryos were cultured in SB431542 (Tocris) beginning at the 4 cell stage. For each cohort of treated embryos, a few embryos were raised to stage 10.5 and to stage 20, to confirm loss of blastopore and of dorsal anterior development.
|
| Growth protocol |
X. tropicalis embryos were generated by in vitro fertilization and were staged according to Nieuwkoop and Faber morphological criteria.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with Trizol reagent, followed by mRNA preparation using oligo-DT Dynabeads (Invitrogen, cat #610.06).
400 ng of mRNA was then used to prepare 3’ RNA-Seq libraries as previously described (Beck et al, PLOS One 2010). Briefly, mRNA was heat sheared for 7 minutes to produce an average fragment size range of 300-500 bp, then used to generate cDNA libraries using a custom oligo dT primer containing Illumina-compatible adapter sequence. cDNA fragments were end-repaired and ligated to standard Illumina adapters. Size-selection was performed using E-gel SizeSelect agarose gels (Invitrogen), products were PCR amplified for 15 cycles, and purified using Ampure XP beads. Library quality was assessed using Bioanalyzer and Qubit, and sequenced on the Genome Analyzer IIx.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
processed data file: 3seq_annotated_called_regions.txt
library strategy: RNA-3seq
|
| Data processing |
Raw counts from 3-SEQ datasets are calculated and annotated to the closest genes using the Unipeak software.
Genome_build: UCSC xenTro2
Supplementary_files_format_and_content: 3seq_annotated_called_regions.txt
|
| |
|
| Submission date |
Mar 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Julie C Baker |
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Baker Lab
|
| Street address |
300 Pastuer Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13741 |
| Series (1) |
| GSE56000 |
Enhancer chromatin signatures predict Smad2/3 binding in Xenopus |
|
| Relations |
| BioSample |
SAMN02691873 |
| SRA |
SRX495661 |
