NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4558121 Query DataSets for GSM4558121
Status Public on Jun 16, 2020
Title stage 19 rep 2
Sample type SRA
 
Source name  whole embryo
Organism Oryzias latipes
Characteristics strain: offspring of d-rR-Tg(olvas-GFP) and Qurt
developmental stage: stage 19
Growth protocol Embryos were incubated at 28 ◦C fresh water for all time course and processed for ATAC-seq at the indicated times
Extracted molecule genomic DNA
Extraction protocol Medaka embryos were grown to the indicated times and chorions were removed by incubating in 1mg/mL Pronase.After removed yorks using deyork buffer,embryo tissues were triturated to homogeneity in 1 mL 1X TrypLE™ Express.
ATAC-Seq libraries were prepared using Omni-ATAC protocol and DNA fragments were recovered using mini-ATAC protocol
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Data processing Adapters were removed using Trimmomatic(version 0.36)
Mapping by Bowtie( version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter
PCR duplicates reads were removed using Picard
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g 7.34e8’
Peak reads counts were calculated by multicov function from BEDTools
Genome_build: medaka ASM223467v1
Supplementary_files_format_and_content: wig files were generated using bamCoverage; Scores represent reads counts
 
Submission date May 18, 2020
Last update date Jun 17, 2020
Contact name Yongjie Liu
E-mail(s) liuyongjie15@mails.ucas.ac.cn
Organization name Institute of Genetics and Developmental Biology
Street address No. 1 West Beichen Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL25587
Series (1)
GSE136027 Dynamic Transcriptional and Chromatin Accessibility Landscape of Medaka Embryogenesis
Relations
BioSample SAMN14945170
SRA SRX8358030

Supplementary file Size Download File type/resource
GSM4558121_AT19-4.final.bw 98.2 Mb (ftp)(http) BW
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