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| Status |
Public on Jul 01, 2022 |
| Title |
S130 |
| Sample type |
genomic |
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| Channel 1 |
| Source name |
DM
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Blood Cell
group id: DM
sample type: input
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was extracted from 9 cell samples using a DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA). The purified gDNA was then quantified and quality assessed by nanodrop ND-1000. Genomic DNA of each sample was sonicated to ~200 – 1000 bp with a Bioruptor sonicator (Diagenode) on “Low” mode for 10 cycles of 30 seconds “ON” & 30 seconds “OFF”. The gDNA and each sheared DNA were aragrose analyzed.
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| Label |
cy3/532
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| Label protocol |
For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.
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| Channel 2 |
| Source name |
DM
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Blood Cell
group id: DM
sample type: IP
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was extracted from 9 cell samples using a DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA). The purified gDNA was then quantified and quality assessed by nanodrop ND-1000. Genomic DNA of each sample was sonicated to ~200 – 1000 bp with a Bioruptor sonicator (Diagenode) on “Low” mode for 10 cycles of 30 seconds “ON” & 30 seconds “OFF”. The gDNA and each sheared DNA were aragrose analyzed.
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| Label |
Cy5/635
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| Label protocol |
For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.
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| Hybridization protocol |
Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).
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| Scan protocol |
According to the manufacturer’s recommendations.
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| Data processing |
Raw data was extracted as pair files by NimbleScan software. We perform Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data was created for each sample. From the normalized log2-ratio data, a sliding-window (750bp) peak-finding algorithm provided by NimbleScan v2.6 (Roche-NimbleGen) is applied to analysis the MeDIP-chip data. A one-sided Kolmogorov-Smirnov (KS) test is applied to determine whether the probes are drawn from a significantly more positive distribution of intensity log2-ratios than those in the rest of the array. Each probe receives a -log10 p-value score from the windowed KS test around that probe (*_pvalues.gff).
If several adjacent probes rise significantly above a set threshold, the region is assigned to an enrichment peak (EP). The peak data files (*_peaks.gff) are generated from the p-value data files (*_pvalues.gff). NimbleScan detects peaks by searching for at least 2 probes above a p-value minimum cutoff (-log10) of 2. Peaks within 500bp of each other are merged.
normalized data file contains: log2 [MeDIP]/[Input]
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| Submission date |
Nov 08, 2021 |
| Last update date |
Jul 01, 2022 |
| Contact name |
Shengqing Hu |
| E-mail(s) |
hsqha@126.com
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| Organization name |
wuhan union hospital
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| Street address |
NO.1277, jiefang road
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| City |
Wuhan |
| State/province |
China |
| ZIP/Postal code |
430022 |
| Country |
China |
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| Platform ID |
GPL16353 |
| Series (1) |
| GSE188395 |
DNA Methylation Profiling Reveals Novel Pathway Implicated in Cardiovascular Diseases of Diabetes |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM5680583_S130_532.pair.gz |
12.0 Mb |
(ftp)(http) |
PAIR |
| GSM5680583_S130_635.pair.gz |
12.0 Mb |
(ftp)(http) |
PAIR |
| Processed data are available on Series record |
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