NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1136305 Query DataSets for GSM1136305
Status Public on May 22, 2015
Title P11_8
Sample type RNA
 
Source name whole blood, P11, week 8
Organism Homo sapiens
Characteristics patient: P11
week: 8
dataset: treatment
tissue: whole blood
Extracted molecule total RNA
Extraction protocol RNA was extracted from Applied Biosystems Tempus Blood RNA Tubes using the Ambion MagMax-96 total RNA Isolation kits. Globin message reduction was conducted using Ambion GlobinClear Human 96 Kits.
Label biotin
Label protocol Biotinylated cRNA were prepared using Illumina Totalprep-96 Amplification Kits with 250ng input.
 
Hybridization protocol Standard Illumina HT-12 V4 hybridization protocol.
Scan protocol Standard Illumina iScan protocol.
Description 6116733004_C
DC3
Total RNA (globin reduced)
Data processing We first applied a normal-exponential convolution model (Xie et al., Bioinformatics, 2009; Shi et al., Nucleic Acids Research, 2010) to correct for the background noise.  An offset of 16 (the default value) was then added to the data (to improve precision and avoid a compression of the fold changes) before they were log2 transformed (to stabilize the variance). Finally, a quantile-quantile normalization was performed. The ComBat method (Johnson et al., Biostatistics, 2007) was used on those normalized data to correct for batch effects (namely a small hybridization chamber effect that was identified through Principal Variance Component Analysis - Li et al., chap. 12, Batch Effects and Noise in Microarray Experiments: Sources and Solutions, Wiley, 2009). At last, only probes which pval detection (provided by Genome Studio) was below 0.01 in at least one sample were kept for analysis.
 
Submission date May 08, 2013
Last update date May 22, 2015
Contact name Jason A Skinner
E-mail(s) jaskinner06@yahoo.com
Organization name Baylor Institute for Immunology Research
Street address 3434 Live Oak
City Dallas
State/province TX
ZIP/Postal code 75204
Country USA
 
Platform ID GPL10558
Series (1)
GSE46734 DALIA-1 Whole Blood Longitudinal Gene Expression

Data table header descriptions
ID_REF
VALUE Non-parametric-normalized batch-corrected log2-transformed signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 5.290331466 0.03116883
ILMN_2055271 4.719093111 0.2298701
ILMN_2383229 4.595549402 0.3441558
ILMN_1806310 5.073451572 0.04545455
ILMN_1653355 4.620545791 0.3298701
ILMN_1705025 5.356741542 0.01948052
ILMN_3241953 4.765017895 0.1922078
ILMN_1668111 4.485228648 0.5571429
ILMN_2295559 4.583718891 0.3662338
ILMN_1680754 4.622402679 0.2896104
ILMN_1659452 5.094633716 0.03896104
ILMN_1767388 4.831555432 0.1454545
ILMN_1698554 4.587690832 0.3662338
ILMN_1814092 5.717450688 0.007792208
ILMN_1760414 4.555336534 0.4337662
ILMN_2061446 5.363772392 0.02727273
ILMN_1676336 5.291861644 0.02727273
ILMN_1752884 4.591703329 0.3181818
ILMN_2270015 4.418499444 0.6857143
ILMN_1726986 5.43044559 0.01818182

Total number of rows: 32978

Table truncated, full table size 1065 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap