NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2579284 Query DataSets for GSM2579284
Status Public on Nov 23, 2017
Title 4Cseq_medaka_EnhZRS
Sample type SRA
 
Source name 48hpf medaka embryos
Organism Oryzias latipes
Characteristics strain: CBA/BL6
developmental stage: 48hpf
tissue: whole embryos
Treatment protocol no treatment
Growth protocol wild type animals, raised in standard laboratory conditions
Extracted molecule genomic DNA
Extraction protocol Chromatin was extracted from single cells preparations from 25 E9.5 mouse embryos or 500 48hpf medaka embryos. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing library strategy: 4C-seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the mm9 and oryLat2 assemblies using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept. Reads located in fragments flanked by two restriction sites of the same enzyme, or in fragments smaller than 40 bp were filtered out
Mapped reads were then converted to reads-per-first-enzyme-fragment-end units, and smoothed using a 30 DpnII fragments mean running window algorithm.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: mm9; oryLat2 (ASM31367v1)
Supplementary_files_format_and_content: bedGraph, they contain smoothened data of 4Cseq of viewpoint that can be directly uploaded to UCSC for visualization.
 
Submission date Apr 17, 2017
Last update date May 15, 2019
Contact name Juan J. Tena
E-mail(s) jjtenagu@upo.es
Organization name CABD/CSIC
Street address Univ. Pablo Olavide, Ctra. Utrera km1
City Sevilla
ZIP/Postal code 41013
Country Spain
 
Platform ID GPL23308
Series (1)
GSE97860 cis-regulatory logic of Shh expression reveals common history of unpaired and paired fins
Relations
BioSample SAMN06759532
SRA SRX2741662

Supplementary file Size Download File type/resource
GSM2579284_4Cseq_medaka_EnhZRS.bedGraph.gz 3.7 Mb (ftp)(http) BEDGRAPH
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