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Sample GSM942930 Query DataSets for GSM942930
Status Public on Jun 05, 2012
Title Replication timing of Tc1-21 in Tc1 MEFs, average of 3 biological replicates
Sample type genomic
 
Channel 1
Source name Early-replicating DNA of Tc1 MEFs
Organism Mus musculus
Characteristics strain: Tc1 (mixed 129/Sv, C57BL/6J, 6Jx129S8)
cell type: Tc1 MEFs
dna replication status: Early-replicating DNA
Extracted molecule genomic DNA
Extraction protocol Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245]. For complete extraction protocol, please refer to PubMed ID: 21637205.
Label Cy5, Cy3, Cy5
Label protocol Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.
 
Channel 2
Source name Late-replicating DNA of Tc1 MEFs
Organism Mus musculus
Characteristics strain: Tc1 (mixed 129/Sv, C57BL/6J, 6Jx129S8)
cell type: Tc1 MEFs
dna replication status: Late-replicating DNA
Extracted molecule genomic DNA
Extraction protocol Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245]. For complete extraction protocol, please refer to PubMed ID: 21637205.
Label Cy3, Cy5, Cy3
Label protocol Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.
 
 
Hybridization protocol Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (6 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 70 bp across human chromosome 21.
Scan protocol GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).
Description Hsa21 data
Three biological replicates: 348297_IMR901_635.pair, 348297_IMR902_532.pair and 348297_Tc1-21MEF3_635.pair raw data files represent the Early-replicating DNA, 348297_IMR901_532.pair, 348297_IMR902_635.pair and 348297_Tc1-21MEF3_532.pair represent the Late-replicating DNA
Data processing NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. For Tc1-21 datasets, early/late data was arranged according to the Tc1-21 sequence (Sequencing data for Tc1-21 is deposited in the ENA database, Study Accession number: ERP000439) prior to smoothing. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].
In this study we analyzed a mouse strain (Tc1) that contains a rearranged human chromosome 21 (Tc1-21). To make sense of Tc1-21 data from a human chromosome 21 array, we reordered the array probes to reflect Tc1-21's rearranged sequence and then processed the data. So some array probes are missing from the processed data file (correspond to deleted regions) while others are found twice (correspond to duplicated regions). The duplicated regions are present in the supplementary processed data (.txt) files on each Sample record.
HSA21_START = Start position of oligo in human chromosome 21 (Hg18, NCBI 36)
HSA21_END = End position of oligo in human chromosome 21 (Hg18, NCBI 36)
Tc1.21_START = Start position of oligo in Tc1 trans-chromosome 21 (Sequencing data for Tc1-21 is deposited in the ENA database, Study Accession number: ERP000439)
 
Submission date Jun 04, 2012
Last update date Jun 05, 2012
Contact name Benjamin Pope
Organization name Florida State University
Department Biological Science
Lab David Gilbert
Street address 319 Stadium Dr
City Tallahassee
State/province FL
ZIP/Postal code 32306-4295
Country USA
 
Platform ID GPL15656
Series (2)
GSE38472 Replication-Timing Boundaries Facilitate Cell-type and Species-specific Regulation of a Rearranged Human Chromosome in Mouse
GSE51334 DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions

Data table header descriptions
ID_REF
VALUE Log2 transformed early/late replication timing ratio

Data table
ID_REF VALUE
CHR21FS009719783
CHR21FS009719853
CHR21FS009720013
CHR21FS009720028
CHR21FS009720123
CHR21FS009721073
CHR21FS009721078
CHR21FS009721418
CHR21FS009721578
CHR21FS009721883
CHR21FS009722248
CHR21FS009722423
CHR21FS009722658
CHR21FS009722663
CHR21FS009722883
CHR21FS009723053
CHR21FS009723058
CHR21FS009723443
CHR21FS009723453
CHR21FS009723608

Total number of rows: 337602

Table truncated, full table size 10572 Kbytes.




Supplementary file Size Download File type/resource
GSM942930_348297_Tc1-21MEF3_532.pair.gz 5.8 Mb (ftp)(http) PAIR
GSM942930_348297_Tc1-21MEF3_635.pair.gz 5.8 Mb (ftp)(http) PAIR
GSM942930_348298_Tc1-21MEF1_532.pair.gz 5.8 Mb (ftp)(http) PAIR
GSM942930_348298_Tc1-21MEF1_635.pair.gz 5.8 Mb (ftp)(http) PAIR
GSM942930_348298_Tc1-21MEF2_532.pair.gz 5.9 Mb (ftp)(http) PAIR
GSM942930_348298_Tc1-21MEF2_635.pair.gz 5.9 Mb (ftp)(http) PAIR
GSM942930_Tc1-21MEF.txt.gz 6.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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