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| Status |
Public on Oct 24, 2014 |
| Title |
Genomic DNA from donor 25 |
| Sample type |
genomic |
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| Source name |
female_pancreatic islet DNA
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| Organism |
Homo sapiens |
| Characteristics |
donor id: donor 25
gender: female
tissue: pancreatic islet
bisuflite conversion batch: 1
illumina chip number: D
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| Growth protocol |
The islets were cultured in CMRL 1066 (ICN Biomedicals, Costa Mesa, CA, USA) supplemented with 10 mM/l HEPES, 2 mM/l L-glutamine, 50 µg/ml gentamicin, 0.25 µg/ml Fungizone (GIBCO, BRL, Gaithersburg, MD, USA), 20 µg/ml ciprofloxacin (Bayer Healthcare, Leverkusen, Germany), and 10 mM/l nicotinamide at 37 °C (5% CO2) for 1–9 days prior to DNA preparation.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from human pancreatic islets using the AllPrep DNA/RNA kit (Qiagen, Hilding, Germany) according to the manufacturer’s instructions. Nucleic acid purity and concentration were determined using a nanodrop (NanoDrop Technologies, Wilmington, DE, USA). All DNA samples had an A260/280 ratio of 1.8-2.1, whereas the 260/280 ratios for RNA were 1.9-2.2. The integrity and quality of the RNA was assessed using the Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and available RIN values from the Bioanalyzer were between 8.6 and 10.
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| Label |
Cy5 and Cy3
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| Label protocol |
Bisulfite Conversion of the DNA was done with the EZ-96 DNA Methylation Kit v1.4. according to the manufacturers instructions (EZ-96 DNA Methylation Kit, cat no D5004, Zymo Research), but no labeling was done
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| Hybridization protocol |
Illumina protocol 15019522 RevB. For XStain process only: 15019521 RevB
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| Scan protocol |
Standard Illumina iScan N240 scanning protocol
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| Description |
Human Pancreatic Islet DNA
I_25
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| Data processing |
The GenomeStudio® methylation module software was used to calculate the raw methylation score for each DNA methylation site, which is represented as methylation β-value. The β-values are calculated as (β= intensity of the methylated allele (M) / intensity of the Unmethylated allele (U) + intensity of the Methylated allele (M) + 100). All samples passed GenomeStudio® quality control steps based on built in control probes for staining, hybridisation, extension and specificity and displayed high quality bisulfite conversion efficiency with an intensity signal above 4000. Probes were then filtered based on Illumina detection p-value, and probes with a mean detection p-value>0.01 were removed from further analysis. In total DNA methylation data were obtained for 483031 probes out of which 3039 probes are non-CpG sites. Since the cohort included islets from both males and females, Y-chromosome data were removed and subsequently DNA methylation data from 482954 probes remained for further analysis. β-values were converted to M-values for further analysis (M = log2 (β / (1 - β)) to remove heteroscedasticity in the data distribution. Background correction and quantile normalization were performed using the lumi package from bioconductor.
The signal_intensities.txt contains Unmethylated and methylated signal intensities
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| Submission date |
Oct 23, 2014 |
| Last update date |
Oct 24, 2014 |
| Contact name |
Charlotte Ling |
| Organization name |
Lund University
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| Department |
Clinical Sciences
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| Lab |
Epigenetics and Diabetes
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| Street address |
Jan Waldenströms gata 35, CRC 91:12
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| City |
Malmö |
| ZIP/Postal code |
20502 |
| Country |
Sweden |
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| Platform ID |
GPL13534 |
| Series (1) |
| GSE62640 |
Analysis of sex differences in DNA methylation in human pancreatic islets |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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