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Sample GSM843869 Query DataSets for GSM843869
Status Public on Dec 06, 2011
Title Replication timing of CM5 myoblasts
Sample type genomic
 
Channel 1
Source name Early-replicating DNA of CM5 myoblasts
Organism Homo sapiens
Characteristics disease status: control
gender: M
cell type: myoblasts
sample type: early replication intermediate
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].
Label 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.
 
Channel 2
Source name Late-replicating DNA of CM5 myoblasts
Organism Homo sapiens
Characteristics disease status: control
gender: M
cell type: myoblasts
sample type: late replication intermediate
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].
Label 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.
 
 
Hybridization protocol Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 1.1 kb across the human genome.
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 Note that across .pair files, all of the design names end in "_HG18_WG_CGH_v3.1_HX3" so the 719690 meaningful probes in each of the .pair files are identical. The different numbers at the beginning of the design name refer to the date it was created by NimbleGen. The only difference is that some of the designs from different dates have different random control probes.
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. 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].
 
Submission date Dec 06, 2011
Last update date Dec 06, 2011
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 GPL14965
Series (2)
GSE34197 DNA Replication Timing is Maintained Genome-wide in Primary Human Myoblasts Independent of D4Z4 Contraction in FSH Muscular Dystrophy
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
CHR01FS000032108 0.244825735971837
CHR01FS000036566 0.242131154215008
CHR01FS000037196 0.241758103655733
CHR01FS000038109 0.241220881819367
CHR01FS000039532 0.240391606182941
CHR01FS000049283 0.234972744649754
CHR01FS000052308 0.233385312008326
CHR01FS000055650 0.231679606055078
CHR01FS000059489 0.229778212083683
CHR01FS000060884 0.229102587023414
CHR01FS000072260 0.223895060826266
CHR01FS000241735 0.204806017569078
CHR01FS000357503 0.245596310674118
CHR01FS000389471 0.263153610720084
CHR01FS000403676 0.27211660669924
CHR01FS000443361 0.30298199799646
CHR01FS000530358 0.390727292580437
CHR01FS000532718 0.393317723662168
CHR01FS000547649 0.409791548364759
CHR01FS000553694 0.416483971078514

Total number of rows: 719690

Table truncated, full table size 24684 Kbytes.




Supplementary file Size Download File type/resource
GSM843869_441205A03_FSHD71510_532.pair.gz 12.3 Mb (ftp)(http) PAIR
GSM843869_441205A03_FSHD71510_635.pair.gz 12.3 Mb (ftp)(http) PAIR
Processed data included within Sample table

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