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Sample GSM1036454 Query DataSets for GSM1036454
Status Public on Sep 07, 2014
Title H2AX_iPSC_4N_positive_PF1
Sample type genomic
 
Channel 1
Source name iPS cell (PF1) genomic DNA
Organism Mus musculus
Characteristics strain: 129Sv/C57 mixed background
Treatment protocol No treatment
Growth protocol culture on feeder with standard media; just before get DNA, split cells on gelatin coated plates.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted with Qiagen Dneasy Blood ans Tissue Kit (Cat No. 69504)
Label Cy5
Label protocol DNA samples were labled with Nimblegen's standard protocol
 
Channel 2
Source name ESC (s1b6a) genomic DNA
Organism Mus musculus
Characteristics strain: 129Sv/C57 mixed background
Treatment protocol No treatment
Growth protocol culture on feeder with standard media; just before get DNA, split cells on gelatin coated plates.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted with Qiagen Dneasy Blood ans Tissue Kit (Cat No. 69504)
Label Cy3
Label protocol DNA samples were labled with Nimblegen's standard protocol
 
 
Hybridization protocol Labeled DNA hybridized to CGH array with Nimblegen's standard protocol
Scan protocol Arrays were scaned with Nimblegen's standard protocol
Description iPSC_PF1_vs_ESC CGH
Data processing Arrays were processed with Nimblegen's standard protocol
 
Submission date Nov 13, 2012
Last update date Sep 08, 2014
Contact name Andrew Zhuo Xiao
E-mail(s) andrew.xiao@yale.edu
Phone 203-785-5111
Organization name Yale Stem Cell Center
Department Genetics
Lab Andrew Xiao
Street address 10 Amistad St
City New Haven
State/province CT
ZIP/Postal code 06519
Country USA
 
Platform ID GPL15225
Series (2)
GSE42266 CNV analysis of iPS cell lines and H2A.X knockout ES cell
GSE42309 H2A.X function in mouse ESC and iPSC (ChIPSeq and CNVs)

Data table header descriptions
ID_REF
EXP_TAWU_518676-159-2-S1B6A_2011-11-11_532
REF_TAWU_518676-159-2-S1B6A_2011-11-11_635
RATIO
EXP_SPATIAL
REF_SPATIAL
RATIO_SPATIAL
EXP_NORM
REF_NORM
VALUE scaled, log2 (Sample/Control) ratio

Data table
ID_REF EXP_TAWU_518676-159-2-S1B6A_2011-11-11_532 REF_TAWU_518676-159-2-S1B6A_2011-11-11_635 RATIO EXP_SPATIAL REF_SPATIAL RATIO_SPATIAL EXP_NORM REF_NORM VALUE
CHR10FS003002777 14.044 13.407 0.637 13.290 13.492 -0.201 13.292 13.440 -0.149
CHR10FS003003474 13.063 12.210 0.853 12.336 12.260 0.075 12.318 12.283 0.035
CHR10FS003009179 12.560 11.933 0.627 11.552 11.661 -0.109 11.558 11.677 -0.119
CHR10FS003012029 12.406 11.484 0.922 11.649 11.481 0.168 11.651 11.488 0.163
CHR10FS003014147 12.747 12.188 0.559 12.048 12.038 0.010 12.036 12.062 -0.026
CHR10FS003018290 13.205 12.283 0.922 12.567 12.519 0.048 12.549 12.536 0.013
CHR10FS003022469 13.527 13.032 0.495 12.873 12.831 0.042 12.858 12.835 0.023
CHR10FS003026571 12.450 11.624 0.826 11.854 11.850 0.004 11.847 11.870 -0.023
CHR10FS003029938 12.942 12.312 0.630 12.208 12.004 0.204 12.192 12.028 0.165
CHR10FS003034088 13.486 12.707 0.780 12.626 12.606 0.020 12.608 12.620 -0.012
CHR10FS003037417 12.255 10.115 2.140 11.642 10.376 1.266 11.644 10.356 1.288
CHR10FS003039460 12.835 11.612 1.223 12.013 11.594 0.419 12.002 11.607 0.395
CHR10FS003042397 12.887 12.076 0.811 12.217 12.152 0.065 12.202 12.176 0.025
CHR10FS003048283 12.925 11.406 1.519 12.314 11.665 0.649 12.296 11.680 0.616
CHR10FS003051779 12.670 12.125 0.545 11.826 11.744 0.081 11.820 11.762 0.058
CHR10FS003056050 13.081 12.562 0.519 12.216 12.350 -0.134 12.200 12.372 -0.172
CHR10FS003056435 11.966 11.185 0.781 11.075 11.042 0.033 11.112 11.033 0.079
CHR10FS003061196 11.968 10.983 0.985 11.396 11.260 0.135 11.411 11.259 0.152
CHR10FS003065272 13.219 12.771 0.448 12.498 12.829 -0.331 12.480 12.833 -0.353
CHR10FS003067612 12.386 11.750 0.636 12.116 11.976 0.140 12.102 11.999 0.103

Total number of rows: 713358

Table truncated, full table size 54282 Kbytes.




Supplementary file Size Download File type/resource
GSM1036454_iPSC_PF1_vs_ESC.txt.gz 27.8 Mb (ftp)(http) TXT
GSM1036454_iPSC_PF1_vs_ESC_532.pair.gz 12.8 Mb (ftp)(http) PAIR
GSM1036454_iPSC_PF1_vs_ESC_635.pair.gz 12.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file
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