Genechip human genome u133 plus 2

Transcription microarray analysis was performed by a GeneChip Human Genome U133 Plus 2.0 transcription microarray (Affymetrix, Santa Clara, CA) as described previously [25 (link)]. The scanned data were processed using GeneChip operating software (Affymetrix). The signal intensity of each probe was normalized so that the mean of the signal intensities of all the probes on a microarray would be 500. The mean of the signal intensities of all probes for a gene was used as the transcription level of the gene. Genes were classified into expressed (> 125) gene and unexpressed (< 125) gene according to their signal intensities.
The information on H3K27me3 modification in gastric mucosa was obtained from GEO (GSM772969). LADs of Tig3 cells [44 (link)] and PrEC cells [36 (link)] were obtained from UCSC Genome Browser and GEO (GSM2610545), respectively.

Fifteen patients with BD all diagnosed according to the revised International Criteria and 14 healthy control subjects were enrolled in the study by Xavier et al [8 (link), 10 (link)]. Total RNA was isolated from peripheral blood mononuclear cells and GeneChip^® Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA, USA) microarrays were used for hybridization [8 (link)]. According to the specifications in its product description, the GeneChip^® Human Genome U133 Plus 2.0 array is a comprehensive whole human genome expression array which covers >47,000 transcripts for expression profiling. The study by Xavier et al was conducted and reported in accordance with the Minimum Information About Microarray Experiment (MIAME) guidelines and both the raw and the processed microarray data were deposited on GEO database with the Series ID GSE17114 [8 (link), 9 , 11 (link), 12 ].

The curation method is summarized in the Supplementary File S3 flowchart and in the Results section. For our analysis we included 34 age-dependent datasets from 32 different studies, 16 included AML and 18 healthy subjects respectively. From the 34 datasets, 32 were produced from Affymetrix GeneChip Human Genome U133 Plus 2.0 (GPL570) and 2 conducted on Affymetrix GeneChip Human Genome U133 Array Set (GPL96 & GPL97) arrays. Table 1 provides detailed information about each dataset, including the number of samples used from each dataset, sample tissue source, as well as the total number of AML patients and healthy subjects. Two studies, GSE12417^{55 (link)} and GSE37642^{56 (link)–59 (link)}, were originally conducted on two different Affymetrix array types (GPL570, and GPL96 & GPL97), so each was separated into two subgroups and each subgroup was considered as individual dataset in our analysis, dataset GSE12417: (i) subgroup 1 included 73 BM and 5 PB samples, and (ii) subgroup 2 included 160 BM and 2 PB. For dataset GSE37642: (i) subgroup 1 included 140 BM and (ii) subgroup 2 included 422 BM samples (Table 1).