GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2428816 Query DataSets for GSM2428816
Status Public on Sep 28, 2017
Title LELS_ChIP-seq_H3K4me3_stage9_replicate2
Sample type SRA
Source name whole embryo
Organism Xenopus laevis
Characteristics developmental stage: NF stage 9
cell type: whole embryo
chip antibody: H3K4me3 (Abcam ab8580)
Growth protocol Embryos were generated using IVF (in vitro fertilization) with outbred animals.
Extracted molecule genomic DNA
Extraction protocol Protein-DNA complexes were isolated with antibody from whole embryo lysates that were fixed, sonicated and yolk depleted.
Libraries were prepared with the Kapa Hyper Prep kit (Kapa Biosystems)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description ChIP-seq of H3K4me3 in stage 9 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 ( 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 GPL17682
Series (1)
GSE92382 Regulatory remodeling in the allo-tetraploid frog Xenopus laevis
BioSample SAMN06141421
SRA SRX2422599

Supplementary file Size Download File type/resource
GSM2428816_LE3LS3_stage9_H3K4me3_3A_peaks.bed.gz 575.9 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap