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Sample GSM4753213 Query DataSets for GSM4753213
Status Public on Oct 27, 2021
Title Low Arsenic exposed subject SC29
Sample type genomic
 
Channel 1
Source name input DNA from human buffy coat
Organism Homo sapiens
Characteristics exposure: Low Arsenic exposed
tissue: buffy coat
chip antibody: none
Extracted molecule genomic DNA
Extraction protocol DNA used for MeDIP-Chip analyses was isolated from buffy coats using standard phenol-chloroform method. The total amount was at least 10 µg DNA, the 260/280 ratio ranged between 1.7-1.9, and the 260/230 ratio appeared higher than 1.6. A total of 57 DNA samples were prepared for the MeDIP-Chip experiments.
Label Cy3
Label protocol Genomic DNA was sonicated to obtain fragments ranging from 200 bp to 600 bp. MeDIP was performed using the MagMeDIP kit (Diagenode, Liège, Belgium) according to the manufacturer’s protocol. In brief, IP incubation mix (containing magbuffer A, magbuffer B, 1.5 µg methylated DNA positive control, 1.5 µg non-methylated DNA negative control) was added to 10 µg of sonicated sample and denatured at 95 °C. 10% of this was kept aside as Input sample and stored at 4°C. Beads were washed 3 times with ice-cold diluted magbuffer A and collected in 20 µl of diluted magbuffer A. The remaining sample was immunoprecipitated using 5µl of antibodymix (containing an antibody against 5’-methylcytidine (provided in the kit) magbuffer A and magbuffer C) and 20 µl of magnetic beads solution. Immunoprecipitation was performed overnight at 4 °C on a rotating wheel. The following day, magnetic beads were washed twice with wash buffer 1 and once with wash buffer 2 and kept on ice. Next, DNA elution was performed using the IPure kit (Diagenode, Liège, Belgium). 50 µl of elution buffer was added to the MeDIP-bead pellet and 92.5 µl to the Input sample and incubated for 15 min at room temperature on a rotating wheel. Supernatant was transferred to a new Eppendorf tube using a magnetic rack at room temperature. Samples were subsequently incubated with 2 µl of glycogen carrier, 100 µl of 100% isopropanol and 15 µl of magnetic beads and incubated for 1 hour at room temperature on a rotating wheel. Magnetic beads were washed using wash buffer 1 and wash buffer 2 for 5 minutes. The DNA was eluted twice by using 75 µl of buffer C and incubated for 15 min at room temperature on a rotating wheel. All the samples were precipitated with sodium acetate and ethanol with glycogen as a carrier for 30 min at -80 °C and centrifuged at max speed for 30 min at 4°C. The cell pellet was washed using 70% ethanol and after air drying suspended in 20µl MQ. 20 ng of both Input and MeDIP samples were used for amplification by whole genome amplification (WGA) using the WGA2 and WGA3 kit (Sigma Aldrich) following the manufacturer’s instruction, without performing the fragmentation step. WGA reactions were cleaned up using silica columns (Sigma Aldrich) and eluted in water. Methylation enrichment in the paired samples MeDIP/Input was derived from qPCR data by calculating the ratio positive control/negative control, applying the ΔΔCq method using the primers included in the kit.
 
Channel 2
Source name medip DNA from human buffy coat
Organism Homo sapiens
Characteristics exposure: Low Arsenic exposed
tissue: buffy coat
chip antibody: monoclonal antibody against 5’-methylcytidine
Extracted molecule genomic DNA
Extraction protocol DNA used for MeDIP-Chip analyses was isolated from buffy coats using standard phenol-chloroform method. The total amount was at least 10 µg DNA, the 260/280 ratio ranged between 1.7-1.9, and the 260/230 ratio appeared higher than 1.6. A total of 57 DNA samples were prepared for the MeDIP-Chip experiments.
Label Cy5
Label protocol Genomic DNA was sonicated to obtain fragments ranging from 200 bp to 600 bp. MeDIP was performed using the MagMeDIP kit (Diagenode, Liège, Belgium) according to the manufacturer’s protocol. In brief, IP incubation mix (containing magbuffer A, magbuffer B, 1.5 µg methylated DNA positive control, 1.5 µg non-methylated DNA negative control) was added to 10 µg of sonicated sample and denatured at 95 °C. 10% of this was kept aside as Input sample and stored at 4°C. Beads were washed 3 times with ice-cold diluted magbuffer A and collected in 20 µl of diluted magbuffer A. The remaining sample was immunoprecipitated using 5µl of antibodymix (containing an antibody against 5’-methylcytidine (provided in the kit) magbuffer A and magbuffer C) and 20 µl of magnetic beads solution. Immunoprecipitation was performed overnight at 4 °C on a rotating wheel. The following day, magnetic beads were washed twice with wash buffer 1 and once with wash buffer 2 and kept on ice. Next, DNA elution was performed using the IPure kit (Diagenode, Liège, Belgium). 50 µl of elution buffer was added to the MeDIP-bead pellet and 92.5 µl to the Input sample and incubated for 15 min at room temperature on a rotating wheel. Supernatant was transferred to a new Eppendorf tube using a magnetic rack at room temperature. Samples were subsequently incubated with 2 µl of glycogen carrier, 100 µl of 100% isopropanol and 15 µl of magnetic beads and incubated for 1 hour at room temperature on a rotating wheel. Magnetic beads were washed using wash buffer 1 and wash buffer 2 for 5 minutes. The DNA was eluted twice by using 75 µl of buffer C and incubated for 15 min at room temperature on a rotating wheel. All the samples were precipitated with sodium acetate and ethanol with glycogen as a carrier for 30 min at -80 °C and centrifuged at max speed for 30 min at 4°C. The cell pellet was washed using 70% ethanol and after air drying suspended in 20µl MQ. 20 ng of both Input and MeDIP samples were used for amplification by whole genome amplification (WGA) using the WGA2 and WGA3 kit (Sigma Aldrich) following the manufacturer’s instruction, without performing the fragmentation step. WGA reactions were cleaned up using silica columns (Sigma Aldrich) and eluted in water. Methylation enrichment in the paired samples MeDIP/Input was derived from qPCR data by calculating the ratio positive control/negative control, applying the ΔΔCq method using the primers included in the kit.
 
 
Hybridization protocol For analysis of DNA methylation levels, the Human DNA Methylation 2.1M Deluxe Promoter Array (Roche NimbleGen) was used. This array has a density of 2.1 million probes (50-75 oligonucleotides long, median probe spacing 100 bp) that represent all annotated human promoters (~ 26,210), 27,867 CpG islands, and 750 miRNA promoters per slide. The promoters and CpG islands largely overlap with transcription start sites of well characterized RefSeq genes, covering, on average, 8 kb upstream and 3 kb downstream. Labeling and hybridization of arrays was performed according to the manufactures’ protocol. In brief, 1 µg of Input DNA and 1 µg of MeDIP DNA were labeled with Cy3 and Cy5 respectively by random priming using the Dual Color DNA labeling kit (Roche NimbleGen). The labeled samples were precipitated using isopropanol and quantified spectrophotometrically using the NanoDrop 1000. 34 µg of Cy3 Input and 34 µg of Cy5 MeDIP DNA were pooled and completely dried by using a speed vac. The pellet was dissolved in hybridization solution using the NimbleGen Hybridization kit. After denaturing, the probe was hybridized overnight on the 2.1M Deluxe Promoter Arrays using the HX1 mixers and the NimbleGen Hybridization system 4. Slides were washed using the NimbleGen wash buffer kit and scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner.
Scan protocol Slides were scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner per manufacturer's protocol.
Data processing Signal intensity data was extracted from the scanned images of each array using NimbleScan v2.6 software and quantile normalized on a per channel basis. Log2 ratios of the intensities were computed (ratio of MeDIP signal / Input signal) and for each array, centering was performed by subtracting the global array bi-weight mean of the log2 ratios such that the computed log2 ratios were centered around 0. Identification of methylated regions was performed using the Probe Sliding Window-ANOVA algorithm (PSW-ANOVA). PSW-ANOVA was implemented in the R statistical programming environment (v2.15.3) (http://www.r-project.org) as a custom script and was provided by Roche NimbleGen. PSW-ANOVA (sliding window of 750 bp comprising 7 probes without selection of a cutoff p-value) was used to identify methylated regions. Peaks were identified in the methylated regions by searching for regions containing at least 8 consecutive probes. Peaks were mapped to promoter regions (from 3 kb upstream to 1 kb downstream of the transcription start site (20) and CpG islands of genes using the NimbleScan v2.6 software.
[CpG_sites_arsenic_Pakistan.txt] Scaled, log2 (medip/Input) ratio for demethylated regions
 
Submission date Aug 29, 2020
Last update date Oct 27, 2021
Contact name Danyel Jennen
E-mail(s) danyel.jennen@maastrichtuniversity.nl
Organization name Maastricht University
Department Toxicogenomics
Street address Universiteitssingel 40
City Maastricht
ZIP/Postal code 6229ER
Country Netherlands
 
Platform ID GPL16284
Series (1)
GSE157111 Genome-wide DNA methylation profiles of Arsenic exposed subjects through drinking water in Pakistan

Supplementary file Size Download File type/resource
GSM4753213_562967_532.pair.gz 43.0 Mb (ftp)(http) PAIR
GSM4753213_562967_635.pair.gz 42.4 Mb (ftp)(http) PAIR
Processed data are available on Series record

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