|
| Status |
Public on Sep 28, 2017 |
| Title |
LETS_ChIP-seq_H3K4me3_stage9_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus tropicalis x 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 tropicalis x 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 |
GPL22797 |
| Series (1) |
| GSE92382 |
Regulatory remodeling in the allo-tetraploid frog Xenopus laevis |
|
| Relations |
| BioSample |
SAMN06141418 |
| SRA |
SRX2422602 |
