|
Status |
Public on Sep 16, 2020 |
Title |
Sox17MO_st11_Rep2 |
Sample type |
SRA |
|
|
Source name |
Whole embryos
|
Organism |
Xenopus tropicalis |
Characteristics |
tissue type: whole embryos at N&F stage 11 organism strain: Nigerian strain
|
Growth protocol |
Developmentally synchronized embryos were generated by in vitro fertilization using standard protocols. Embryos were incubated in agarose-coated dishes in 1/9thX MMR at 25oC until needed.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Embryos were injected with Total RNA was isolated at indicated stages using a Nucleo-spin RNA kit (Machery-Nagel). RNA-seq libraries were generated using Smart-seq2 cDNA synthesis followed by tagmentation (Picelli et al., 2014).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Sox17 MO-injected stage 11 embryo RNA-seq replicate 2
|
Data processing |
ChIP-seq raw reads were assessed by FastQC and trimmed with Trimmomatic. Reads were aligned to the Xenopus tropicalis genome assembly version 9.0 using bowtie2 v2.3.4.7. Duplicate and multi-mapped reads were removed by Picard and samtools. Peaks were called with MACS2 against NF10.5 input DNA with default options. Peaks were associated with genes using the HOMER “nearest TSS function. High confidence ChIP-seq peaks were identified using Irreproducible discovery rate (IDR) analysis sing a threshold of 0.01. RNA-seq raw reads were assessed using FastQC and adapters/low quality reads were removed with Trimmomatic. Reads were mapped to the Xenopus tropicalis genome version 9.0 with bowtie2. Mapped reads were quantified using RSEM and reported in transcripts per million (TPM). Differentially expressed genes (LogFC ><= |1| and FDR <= 0.05) were identified by a pairwise comparison between control-MO and Sox17-MO, control-MO and Bcat-MO embryos at each stage using RUVSeq (R package). Genome_build: Xenopus tropicalis v9.0
|
|
|
Submission date |
Apr 15, 2020 |
Last update date |
Sep 16, 2020 |
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 |
GPL21875 |
Series (1) |
GSE148726 |
Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endodermal gene regulatory network |
|
Relations |
BioSample |
SAMN14601808 |
SRA |
SRX8119351 |