Gene expression profiling was performed using Affymetrix Human Gene 1.0 (cohort 3, previously presented in (Arner et al., 2012 (link))) and Affymetrix Human Gene 1.1 (EBF1 knockdown vs. control) ST arrays (Affymetrix, Inc., Santa Clara, CA). Data were analyzed with packages available from Bioconductor (www.bioconductor.org ). Normalization and calculation of gene expression was performed with the Robust Multichip Average expression measure using oligo package (Carvalho and Irizarry, 2010 (link)). Prior to further analysis, a non-specific filter was applied to include genes with expression signal >30 in at least 20% of all samples. Limma package (Smyth, 2004 (link)) was used to identify the differentially expressed genes which were ranked in the gene set enrichment analyses and principal component analysis was performed using the FactomineR package. Motif activity response analysis (MARA) was performed exactly as described (Arner et al., 2012 (link); Suzuki et al., 2009 (link)) and detailed in SEP.
Human gene 1
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Human Gene 1.1 is a laboratory equipment designed for the analysis and study of human genes. It provides researchers with the tools necessary to perform various genetic analysis techniques. The core function of this product is to facilitate the detection, quantification, and examination of specific human genetic sequences.
Automatically generated - may contain errors
Lab products found in correlation
Wt sense target labeling kit, by Thermo Fisher Scientific (2 mentions)
1.1 st arrays, by Thermo Fisher Scientific (2 mentions)
Gs 3000, by Thermo Fisher Scientific (2 mentions)
Gene titan scanner, by Thermo Fisher Scientific (2 mentions)
Paxgene blood mirna kit, by Preanalytix (1 mentions)
Qiacube, by Qiagen (1 mentions)
Genechip human genome u133 plus 2, by Thermo Fisher Scientific (1 mentions)
5 protocols using human gene 1
1
Affymetrix Gene Expression Profiling
2
Whole Blood RNA Profiling for Transcriptomics
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Total RNA was extracted from PAXgene blood on the QIAcube (Qiagen, Germany), using the PAXgene Blood miRNA kit from PreAnalytix, according to manufacturer’s instructions. Human Gene 1.1 (GPL6244; RTP and CHFP cohorts) ST array plates (Affymetrix, United States) were used to measure mRNA abundance. This work was carried out at The Scripps Research Institute DNA Array Core Facility (TSRI; La Jolla, CA). The resulting CEL files were processed using the ‘oligo’ R package [20 (link)].
3
Profiling PTH1R Expression in Breast Cancer
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To study the expression of PTH1R in breast cancer tumors, we identified publicly available microarray data sets from the NCBI and GEO data repositories. The following keywords were used to search the data repositories: breast cancer, bone metastasis, human, murine, gene expression profiling by array. Data sets were further filtered to exclude studies that included drug treatments and metastasis to organs other than bone. Thirty data sets were found, of which 10 studies (n = 3 murine and 7 human) fit the required criteria. They included GDS4077, GDS5666, GSE21444, GDS4091, GSE137842, GDS3853, GSE8977, GSE9014, GDS4761, and GSE57947. All data sets were on an Affymetrix GeneChip Human Genome U133 Plus 2.0 or Affymetrix Human Gene 1.1 platform. Data analysis and statistical analysis were conducted using GEO2R (an online data analysis tool used to analyze GEO data sets under the same experimental conditions), and raw data were retrieved from individual data files as bar charts.
4
Gene Expression Analysis Using Affymetrix Arrays
5
Gene Expression Analysis Using Affymetrix Arrays
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Aliquots of total RNA (200ng) were labeled using Ambion WT sense Target labeling kit and hybridized to Human Gene 1.0 or 1.1 ST Arrays (Affymetrix) as described. After washing, arrays were scanned using a GS 3000 or Gene Titan scanner (Affymetrix) as appropriate.
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