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Sample GSM1099773 Query DataSets for GSM1099773
Status Public on Mar 18, 2013
Title iPSC
Sample type genomic
 
Channel 1
Source name reprogrammed somatic cells
Organism Mus musculus
Characteristics cell type: in vitro reprogrammed somatic cells
restriction enzyme: MspI
time point: iPSC
Extracted molecule genomic DNA
Extraction protocol Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)
Label Cy3
Label protocol Random 9-mers pre-labeled with either Cy3 or Cy5
 
Channel 2
Source name reprogrammed somatic cells
Organism Mus musculus
Characteristics cell type: in vitro reprogrammed somatic cells
restriction enzyme: HpaII
time point: iPSC
Extracted molecule genomic DNA
Extraction protocol Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)
Label Cy5
Label protocol Random 9-mers pre-labeled with either Cy3 or Cy5
 
 
Hybridization protocol See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details
Scan protocol Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
Data processing Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII and MspI signals are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167). After intra-array normalization each channel was centered by subtracting background noise (2.5 median absolute deviations from the median of the random probes’ log2 signal for that channel) from its log2-transformed signal intensities. The HpaII/MspI (unmethylated/reference) ratio was then determined for each probe set on array.
 
Submission date Mar 18, 2013
Last update date Mar 18, 2013
Contact name Ben S. Wittner
E-mail(s) wittner.ben@mgh.harvard.edu
Organization name Massachusetts General Hospital
Department Center for Cancer Research
Lab Lawrence
Street address 149 13th Street
City Boston
State/province MA
ZIP/Postal code 02129
Country USA
 
Platform ID GPL10283
Series (2)
GSE42478 Defining a molecular roadmap of cellular reprogramming into iPS cells
GSE45248 Defining a molecular roadmap of cellular reprogramming into iPS Cells [DNA methylation]

Data table header descriptions
ID_REF
VALUE log2 Ratio (HpaII/MspI)

Data table
ID_REF VALUE
MM5MSPIS00000029 0.428155201
MM5MSPIS00000030 2.430569397
MM5MSPIS00000131 -0.752301683
MM5MSPIS00000132 -1.439652518
MM5MSPIS00000259 2.021560927
MM5MSPIS00000260 0.294646155
MM5MSPIS00000282 1.139359713
MM5MSPIS00000285 1.984103154
MM5MSPIS00000335 0.44117224
MM5MSPIS00000336 -0.749444181
MM5MSPIS00000388 -0.897394097
MM5MSPIS00000438 -2.238987404
MM5MSPIS00000452 -2.552146828
MM5MSPIS00000453 -2.366883058
MM5MSPIS00000558 0.209619241
MM5MSPIS00000622 1.654095278
MM5MSPIS00000718 3.211395489
MM5MSPIS00000719 2.749556227
MM5MSPIS00000826 -0.995994715
MM5MSPIS00000939 -0.793926868

Total number of rows: 25720

Table truncated, full table size 735 Kbytes.




Supplementary file Size Download File type/resource
GSM1099773_341814_635.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM1099773_341814_MM5_532.pair.gz 6.3 Mb (ftp)(http) PAIR
Processed data included within Sample table

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