|
Status |
Public on Nov 03, 2017 |
Title |
Bone Marrow, BALB/c, 8 week old |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
MeDIP enriched genomic DNA
|
Organism |
Mus musculus |
Characteristics |
strain: BALB/c tissue: Bone Marrow
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Hearts from 1-day, 7-day, 2-week old mice of C57BL6/J murine strain were purchased from the Tri-City's Academic Animal Experiment Centre of the Medical University of Gdańsk. Hearts for 8-week-old mice of C57BL/6J murine strain were purchased form the Jackson Laboratories. Genomic DNA was isolated using DNeasy Blood&Tissue Kit (QIAGEN).
|
Label |
Cy3
|
Label protocol |
DNA labeling and hybridization was performed according to NimbleGen’s protocol with our modifications. The immunoprecipitated CpG methylated DNA (test) and the untreated, sonicated DNA (input control) were labeled by using the random priming with the Nimblegen Dual-Color DNA Labeling kit (Roche-Nimblegen, cat. No. 06370250001) with fluorescent dyes Cy3 and Cy5, respectively.
|
|
|
Channel 2 |
Source name |
input DNA
|
Organism |
Mus musculus |
Characteristics |
strain: BALB/c tissue: Bone Marrow
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Hearts from 1-day, 7-day, 2-week old mice of C57BL6/J murine strain were purchased from the Tri-City's Academic Animal Experiment Centre of the Medical University of Gdańsk. Hearts for 8-week-old mice of C57BL/6J murine strain were purchased form the Jackson Laboratories. Genomic DNA was isolated using DNeasy Blood&Tissue Kit (QIAGEN).
|
Label |
Cy5
|
Label protocol |
DNA labeling and hybridization was performed according to NimbleGen’s protocol with our modifications. The immunoprecipitated CpG methylated DNA (test) and the untreated, sonicated DNA (input control) were labeled by using the random priming with the Nimblegen Dual-Color DNA Labeling kit (Roche-Nimblegen, cat. No. 06370250001) with fluorescent dyes Cy3 and Cy5, respectively.
|
|
|
|
Hybridization protocol |
The combined test and input DNA samples were suspended in hybridization buffer (Roche, cat. no. 05583683001) cohybridized onto Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Arrays for 20 hr at 42°C, following washing with Nimblegen Wash Kit (Roche cat. no. 05584507001).
|
Scan protocol |
The image was acquisited with MS200 Scanner (Roche, NimbleGen) at 2 µm resolution by using high-sensitivity and autogain settings.
|
Description |
Genomic DNA methylation profile in the bone marrow of the BABL/c mouse
|
Data processing |
The data from scanned images were extracted and processed with NimbleScan (2.6.0.0) (Roche, Nimblegen) using default parameters. Data processing included quantile normalization of each chanel separately, obtaining log2 ratios, P-scores and peak identification. Log2 ratios represent the ratios of the immunoprecipitated DNA signal to the input DNA signal. The mean log2 ratios were calculated using a Tukey biweight mean. P-scores were calculated from log2 ratios by performing sliding-window (750 bp) Kolmogorov-Smirnov (KS) test around each probe applied to determine -log10 p-value from the windowed KS test around that probe. The methylation peaks were obtained by merging consecutive probes with P scores over the assumed cut-off (default 2.0) with maximum 500 bp spacing and minimum of two probes per peak.
|
|
|
Submission date |
Nov 03, 2016 |
Last update date |
Nov 03, 2017 |
Contact name |
Pawel Sachadyn |
E-mail(s) |
psach@pg.gda.pl
|
Phone |
+48 583471605
|
Organization name |
Gdansk University of Technology
|
Department |
Molecular Biotechnology and Microbiology
|
Street address |
Narutowicza 11/12
|
City |
Gdansk |
ZIP/Postal code |
80-233 |
Country |
Poland |
|
|
Platform ID |
GPL15761 |
Series (1) |
GSE89518 |
DNA methylation profiling of mouse tissues |
|