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Sample GSM3737012 Query DataSets for GSM3737012
Status Public on Dec 27, 2019
Title CD34negCD19posCB14DAPI-Early S Fraction
Sample type SRA
 
Source name cord blood pool 14 CD34-CD19+ fraction
Organism Homo sapiens
Characteristics s phase fraction: Early S fraction
gender: not applicable
replicate: 2
Treatment protocol Asynchronous cells were labeled with 100 micromolar BrdU for 2 hours at 37˚C in RPMI 1640+ 10% FBS
Growth protocol Cell lines were cultured in RPMI1640+10-20% FBS
Extracted molecule genomic DNA
Extraction protocol Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011; Marchal et al., 2017). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed by either microaray or 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
 
Data processing Genome-wide RT profiles were constructed by Repli-chip, Repli-seq, Capture Repli-seq and deep whole genome sequencing (WGS). Replication timing profiles were scaled and pooled for analysis as previously described (Ryba et al., 2011; Marchal et al., 2018). Briefly, Log2 transformed early/late replication timing ratios were quantile normalized and loess smoothed in R
Genome_build: HG38
Supplementary_files_format_and_content: processed data are 50kb windows in HG38 genome.
 
Submission date Apr 26, 2019
Last update date Dec 27, 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 GPL16791
Series (2)
GSE130373 Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture [Repli-Seq]
GSE130374 Replication timing alterations in leukemia reflect stable clinically-relevant changes in genome architecture
Relations
BioSample SAMN11514988
SRA SRX5758050

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

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