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Sample GSM4477775 Query DataSets for GSM4477775
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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