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Sample GSM2337695 Query DataSets for GSM2337695
Status Public on Feb 28, 2017
Title FG DMH1 rep 2
Sample type SRA
 
Source name FG_DMH1
Organism Xenopus laevis
Characteristics Stage: NF20
tissue: Foregut explants
genotype/variation: wild type
treatment: DMH1
Treatment protocol Small molecule inhibitors were dissolved in DMSO and embryos were cultured from stages NF12-20 with either DMSO vehicle in 0.1XMBS or 40 μM DMH1 (TOCRIS) or BIO (60 μM; TOCRIS). To activate the hsp:Dkk1GFP transgene, we gave a pulse of 30min in 37C followed by incubation at 13C.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from two or three independent biological replicates using the Nucleo-spin RNA kit (Machery-Nagel).
Libraries were constructed with TruSeq Stranded mRNA Library Prep Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Quality check and trimming of raw reads was performed using FastQC and Trimmomatic, respectively at default parameters. Quality trimmed Reads were mapped to the X. laevis genome 9.1 and quantified using RSEM at default parameters.
Genome_build: Xenopus laevis genome v9.1
Supplementary_files_format_and_content: Matrix with genes and samples providing expression of genes in each sample in TPM(Transcripts per Million). File is in .xlsx format
 
Submission date Oct 05, 2016
Last update date May 15, 2019
Contact name Aaron M Zorn
E-mail(s) aaron.zorn@cchmc.org
Phone 636 3770
Organization name Cincinnati Children's Hospital Medical Center
Department Develpomental Biology
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45236
Country USA
 
Platform ID GPL18936
Series (2)
GSE87653 Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors [RNA-seq]
GSE87654 Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors
Relations
BioSample SAMN05864178
SRA SRX2213239

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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