DNA promoter methylation data were available for H2AX and HMGB1 in a total of n=77 individuals from a previously published dataset.18 (link) Briefly, genome-wide promoter methylation data were obtained using MeDIP (methylated DNA immunoprecipitation) and subsequently analyzed by using the Human Promoter 1.0R Array (Affymetrix, Santa Clara, California, USA) technology. Gene expression data from the same cohort were extracted from a previously published genome-wide expression data set18 (link) from n=55 (SAT) and n=48 (OVAT) with n=41 overlapping data for SAT and OVAT. RNA integrity was validated by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, California, USA) and genome-wide mRNA expression data have been generated using human HT-12 gene expression arrays. Only samples with RNA integrity values of more than five were included for further analysis.
Human promoter 1.0r array
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Human Promoter 1.0R Array is a lab equipment product designed for the analysis of human promoter regions. It provides comprehensive coverage of the human genome's promoter regions, enabling researchers to study gene regulation and expression patterns.
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Lab products found in correlation
4 protocols using human promoter 1.0r array
1
Promoter Methylation and Gene Expression Analysis
2
Comparative Transcriptomics of LSD1 and MYC Knockdown in Mouse and Human ESCs
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Previously published data from LSD1 knockout and WT mouse ESC samples measured using Illumina MouseWG-6 v2.0 expression beadchip were downloaded from the NCBI Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/ ) with accession numbers GSE21131 (Foster et al., 2010 (link)). Log2 fold change for each gene was then calculated by averaging across duplicates in either LSD1 KD or WT samples and subtracting log2 transformed values in LSD1 KD measurement with WT measurement. The same approach was taken to process data from MYC knockdown and WT mouse ESC samples measured using Illumina HiSeq 2500 (GSE113329 (Seruggia et al., 2019 (link))) and microarray data from LSD1 knockdown and WT human ESC samples measured using Affymetrix Human Promoter 1.0R Array from human ESCs (GSE24844 )(Adamo et al., 2011 (link)). RNA-seq data from ESCs in naïve state (GSE117896 ) was used for defining expressed genes (Yang et al., 2019 (link)). Specifically, expressed genes were defined as any gene with regularised log expression equal or higher than 5.
3
ChIP-Chip Analysis of C-JUN and C-FOS Targets
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To identify the promoter targets of C-JUN and C-FOS, we used SimpleChIP Enzymatic Chromatin IP kit (Magnetic Beads) to perform chromatin immunoprecipitation (ChIP) assays according to the manufacturer’s instructions (Cell Signaling Technology, MA, USA), followed by a promoter chip array assay (Affymetrix, CA, USA). Briefly, chromatin from the MCF7 and HMEC cell lines, which was previously prepared and digested with micrococcal nuclease, was incubated with 2 μg of C-JUN antibody, C-FOS antibody (Santa Cruz Biotechnology, TX, USA) or the negative immunoprecipitation control normal anti-IgG rabbit antibody (#2729, Cell Signaling Technology, MA, USA). Then, the immunoprecipitated DNA was purified according to the manufacturer's instructions (Affymetrix CA, USA) and subsequently hybridized to a Human Promoter 1.0R Array (Affymetrix, CA, USA). After that, the arrays were washed, stained and scanned according to the manufacturer’s protocols.
4
Differential Gene Expression Analysis of LSD1 and MYC Knockdown in Mouse and Human ESCs
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Previously published data from LSD1 knockout and WT mouse ESC samples measured using Illumina MouseWG-6 v2.0 expression beadchip were downloaded from the NCBI Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE21131 45 (link) . Log2 fold change for each gene was then calculated by averaging across duplicates in either LSD1 KD or WT samples and subtracting log2 transformed values in LSD1 KD measurement with WT measurement. The same approach was taken to process data from MYC knockdown and WT mouse ESC samples measured using Illumina HiSeq 2500 (GSE113329 74 (link) ) and microarray data from LSD1 knockdown and WT human ESC samples measured using Affymetrix Human Promoter 1.0R
Array from human ESCs (GSE24844) 46 (link) . RNA-seq data from ESCs in naïve state (GSE117896) was used for defining expressed genes 75 (link) . Specifically, expressed genes were defined as any gene with regularised log expression equal or higher than 5.
Array from human ESCs (GSE24844) 46 (link) . RNA-seq data from ESCs in naïve state (GSE117896) was used for defining expressed genes 75 (link) . Specifically, expressed genes were defined as any gene with regularised log expression equal or higher than 5.
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