NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2496040 Query DataSets for GSM2496040
Status Public on Jul 28, 2017
Title Repli-seq F121-9 hybrid mouse cells - Early S fraction - Rep 1
Sample type SRA
 
Source name mESC
Organism Mus musculus
Characteristics strain background: F1 CASTx129 hybrid mouse (clone F121-9)
cell line/type: ES cells
s phase fraction: Early S fraction
replicate: 1
Growth protocol 46C mESCs were cultured in mESC media supplemented with LIF. F121-9 ESC were cultured in N2B27+2i+LIF media.
Extracted molecule genomic DNA
Extraction protocol Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed either by NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370). 
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description processed data file:
F121-9_nesc_r1_R_T_.bedGraph
F121-9_nesc_r1_R_T_Loess.bedGraph
F121-9_nesc_r1_R_T_qnorm.bedGraph
F121-9_nesc_r1_T_clip_129_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph
F121-9_nesc_r1_T_clip_cas_genparsed_mm10w50000gt100snp_unified_qnorm_loess0-01.bedGraph
Data processing Reads are mapped on mm10 using bowtie2. F121-9 cells have also been parsed, between cas and 129 genome (“*cas*” and “*129*” files)
Coverage data are calculated from mapped reads using samtools and bedtools
Base 2 log of early to late coverage ratio is calculated on 50kb windows (“*_T_.bg” files)
Log Ratio data are quantile normalized using R package preprocessCore (“*_T_qnorm.bg” files)
Data are smoothed using R Loess function (“*_T_Loess.bg” files, and “*unified_qnorm_loess0-01.bg” files for allele specific data)
Genome_build: mm10
Supplementary_files_format_and_content: processed data are coverage data on mm10 genome, they can be visualized using a genome viewer. To visualize them using UCSC genome viewer, add a bedgraph file header (see UCSC website for description of the header)
 
Submission date Feb 20, 2017
Last update date May 15, 2019
Contact name David M Gilbert
Organization name Florida State University
Department Biology
Lab Gilbert
Street address 319 Stadium Drive
City Tallahassee
State/province FL
ZIP/Postal code 32306-4295
Country USA
 
Platform ID GPL17021
Series (2)
GSE95091 Repli-seq: genome-wide analysis of replication timing by next-generation sequencing
GSE95092 genome-wide analysis of replication timing by repli-chip and repli-seq
Relations
BioSample SAMN06349388
SRA SRX2577311

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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