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Sample GSM2375113 Query DataSets for GSM2375113
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

Supplementary file Size Download File type/resource
GSM2375113_BcBMr_532.pair.gz 12.4 Mb (ftp)(http) PAIR
GSM2375113_BcBMr_635.pair.gz 12.5 Mb (ftp)(http) PAIR
Processed data are available on Series record

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