|
| Status |
Public on Jan 01, 2020 |
| Title |
SPNT HCC 1 [Methylation] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
input DNA from SPNT HCC 1
|
| Organism |
Mus musculus |
| Characteristics |
cohort: SPNT HCC
replicate: 1
fraction: input DNA
|
| Treatment protocol |
Vehicle control by oral gavage for 2 years
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were isolated from these selected samples using the DNeasy kit® (Qiagen, Valencia, CA) and Invitrogen PureLink Mini Kit® (Life Technologies Corporation, Carlsbad, CA), respectively, and stored at -80C. DNA were quantified by using a NanoDrop® (ThermoScientific, Wilmington, MA),
|
| Label |
cy3
|
| Label protocol |
The high molecular weight genomic DNA was sonicated to generate 200-500bp sized DNA fragments using a Bioruptor sonicator® (Diagenode, Denville, NJ) using cycle conditions of 30 sec on/90 sec off for a total duration of 12.5 minutes. Methylated DNA molecules were enriched by binding to the MBD2B/MBD3L1 complex using the MethylCollector Ultra kit® (Active Motif, Carlsbad, CA) according to the manufacturer’s protocol. Input and enriched methylated-DNA fragments from the same sample were whole genome amplified (WGA) using a WGA2 kit® (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s protocol
|
| |
|
| Channel 2 |
| Source name |
methylated DNA from SPNT HCC 1
|
| Organism |
Mus musculus |
| Characteristics |
cohort: SPNT HCC
replicate: 1
fraction: methylated DNA
|
| Treatment protocol |
Vehicle control by oral gavage for 2 years
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were isolated from these selected samples using the DNeasy kit® (Qiagen, Valencia, CA) and Invitrogen PureLink Mini Kit® (Life Technologies Corporation, Carlsbad, CA), respectively, and stored at -80C. DNA were quantified by using a NanoDrop® (ThermoScientific, Wilmington, MA),
|
| Label |
cy5
|
| Label protocol |
The high molecular weight genomic DNA was sonicated to generate 200-500bp sized DNA fragments using a Bioruptor sonicator® (Diagenode, Denville, NJ) using cycle conditions of 30 sec on/90 sec off for a total duration of 12.5 minutes. Methylated DNA molecules were enriched by binding to the MBD2B/MBD3L1 complex using the MethylCollector Ultra kit® (Active Motif, Carlsbad, CA) according to the manufacturer’s protocol. Input and enriched methylated-DNA fragments from the same sample were whole genome amplified (WGA) using a WGA2 kit® (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s protocol
|
| |
|
| |
| Hybridization protocol |
The labeling of WGA IP and input DNA, microarray hybridization, and scanning were performed at the Florida State University genomics core laboratory following the described protocol (Roche NimbleGen (2010)).
|
| Scan protocol |
Data were extracted from scanned images using NimbleScan 2.4 extraction software (NimbleGen Systems, Inc., Madison, WI)
|
| Description |
Methylation Signal for SPNT HCC 1
|
| Data processing |
The probe-level log2(Cy5/Cy3) values were normalized using Lowess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173. These signal values were further quantile normalized to adjust for between sample variations. DETAILS: The GC Lowess method utilizes both 'Cy3' and 'Cy5' values as following: * Classify probes into bins according to CG content (proportion of number of C and G nucleotides in probe sequence) * For each CG content bin (k), we fit lowess regression to predict log2(Cy5/Cy3)_k value using log2(sqrt(Cy3*Cy5))_k value * Compute normalized value = sigma_bar *(observed log2(Cy5/Cy3)_k - predicted log2(Cy5/Cy3)_k)/sigma_k, where sigma_k is mean absolute deviation of (observed log2(Cy5/Cy3)_k - predicted log2(Cy5/Cy3)_k) and sigma_bar is geometric mean of all sigma_k's. This normalization corrects for both dye bias and CG bias simultaneously.
|
| |
|
| Submission date |
Jun 11, 2019 |
| Last update date |
Jan 02, 2020 |
| Contact name |
Deepak Mav |
| Organization name |
Sciome LLC
|
| Street address |
2 Davis Drive
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL15761 |
| Series (2) |
| GSE132577 |
Genome-wide promoter DNA Methylation Profiling of Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Exposure to Ginkgo biloba Extract (GBE) in B6C3F1/N Mice [Methylation] |
| GSE132578 |
Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Exposure to Ginkgo biloba Extract (GBE) in B6C3F1/N Mice |
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