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Sample GSM2428813 Query DataSets for GSM2428813
Status Public on Sep 28, 2017
Title Xenopus_laevis_RNAseq_stage10.5_replicate1
Sample type SRA
 
Source name whole embryo
Organism Xenopus laevis
Characteristics developmental stage: NF stage 10.5
cell type: whole embryo
Growth protocol Embryos were generated using IVF (in vitro fertilization) with outbred animals.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 20 Nieuwkoop-Faber stage 10.5 embryos (two biological replicates) using Trizol and Qiagen columns. 4-5 ug of total RNA was treated with DNase I on column and depleted of rRNA (ribosomal RNA) using Magnetic gold RiboZero RNA kit (Illumina) resulting in a yield of 45 - 52 ng of rRNA depleted total RNA.
2 ng of rRNA-depleted total RNA was reserved for Experion (Bio-Rad) quality assessment run for rRNA depletion and the remaining was used for first and second strand synthesis (strand-specific protocol). Total yield of dscDNA was between 14.5-15.8 ng and out of this 1.2 - 5 ng was used for sample preparation for high high-throughput sequencing (according to manufacturer's protocol).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Total RNA (rRNA depleted) of stage 10.5 Xenopus laevis embryos
Data processing ChIP-seq and genomic DNA reads were aligned to the genome using bwa version 0.7.10-r789 with default parameters
Duplicates in genomic DNA were marked using Picard MarkDuplicates version 2.7.1
ChIP-seq peaks were called using macs2 version 2.0.10 with qvalue cutoff=1e-03 relative to respective ChIP input track.
RNA-seq reads were mapped to genome Xla.v91 + transcriptome v1.8 (http://www.xenbase.org) using STAR version 2.4.2a with --quantMode TranscriptomeSAM. Quantification was performed on the reads mapped to the transcriptome by STAR using eXpress v1.5.1.
Genome_build: Xenopus tropicalis: xt9.0; Xenopus laevis: Xla.v91; Xenopus tropicalis x Xenopus laevis: xt9.0 + Xla.v91 (merged)
Supplementary_files_format_and_content: Results from eXpress (.xprs); peak files in BED format.
 
Submission date Dec 14, 2016
Last update date May 15, 2019
Contact name Simon van Heeringen
E-mail(s) s.vanheeringen@science.ru.nl
Phone +31-24-3610560
Organization name Radboud University
Department Molecular Developmental Biology
Street address Geert Grooteplein 28
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
 
Platform ID GPL17682
Series (1)
GSE92382 Regulatory remodeling in the allo-tetraploid frog Xenopus laevis
Relations
BioSample SAMN06141424
SRA SRX2422596

Supplementary file Size Download File type/resource
GSM2428813_RNAseq_stage10.5_xlaevis_replicate1.xprs.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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