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Sample GSM2428811 Query DataSets for GSM2428811
Status Public on Sep 28, 2017
Title Xenopus_tropicalis_genomic
Sample type SRA
Source name whole embryo
Organism Xenopus tropicalis
Characteristics developmental stage: NF stage 18
cell type: whole embryo
Growth protocol Embryos were generated using IVF (in vitro fertilization) with outbred animals.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated.
DNA was sonicated to 200-700bp fragments, 300bp fragments were size-selected.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Description Genomic DNA of Xenopus tropicalis 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 ( 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
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 GPL21874
Series (1)
GSE92382 Regulatory remodeling in the allo-tetraploid frog Xenopus laevis
BioSample SAMN06141426
SRA SRX2422594

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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