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Sample GSM946858 Query DataSets for GSM946858
Status Public on Jan 22, 2013
Title Big lung tumor tissue with Dnmt3a intact
Sample type SRA
Source name lung tumors
Organism Mus musculus
Characteristics genotype/variation: WTB
Treatment protocol adenoviral Cre recombinase was delivered to mice of 6-12 weeks old via intratracheal or intranosal approach
Growth protocol K-ras LSL-G12D mice were crossed with the Dnmt3a conditional KO mice. After adenoviral Cre recombinase –mediated recombination, mice were generated with lung cells that carried the K-ras G12D mutation and were homozygous (KO) and WT at the Dnmt3a locus. Tumors were flash-frozen in liquid nitrogen and stored at -80°C.
Extracted molecule genomic DNA
Extraction protocol 5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
Data processing Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: (part of bsmap package)
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph-format containing the genomic methylation ratios of the respective sample
Submission date Jun 12, 2012
Last update date May 15, 2019
Contact name Guenter Raddatz
Organization name German Center for Cancer Research
Street address Im Neuenheimer Feld 580
City Heidelberg
ZIP/Postal code 69120
Country Germany
Platform ID GPL13112
Series (1)
GSE38651 Dnmt3a protects active chromosome domains against cancer-associated hypomethylation
SRA SRX153157
BioSample SAMN01047960

Supplementary file Size Download File type/resource
GSM946858_wtb.bedgraph.gz 183.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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