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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 04, 2018 |
| Title |
CCTt8 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C3H/HeN
tissue: liver
age: 74 weeks
normal or tumor: tumor
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissues were lysed in lysis buffer, treated with RNase, and purified with a phenol-chloroform mixture
RRBS libraries were prepared from genomic DNA of 3 normal liver tissues and 3 tumor tissues having a Ha-ras mutation according to the protocol reported by Boyle et al (Genome Biol. 2012, 13:R92. doi: 10.1186/gb-2012-13-10-r92). with some modifications. Briefly, 100 ng of genomic DNA was digested with MspI, subjected to gapfilling and A-tailing, and ligated with TruSeq adaptors included in the TruSeq DNA Sample Prep Kit (FC-121-1001, Illumina). After DNA size selection and ligation efficiency were checked, adaptor-ligated DNA was subjected to bisulfite conversion and amplified by PCR. The PCR products were cleaned-up using Agencourt AMPure XP beads
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Bisulfite-treated sequencing reads were aligned by a paired-end alignment method for a unique best hit to the mouse reference genome (NCBI/mm10) using the Bismark program
adapter trimming and quality control was performed using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The aligned data were used for analyzing DNA methylation profiles using a methylKit package on R
The aligned data were used for analyzing DNA methylation profiles using a methylKit package on R
DMCs were extracted using methylKit for the cytosines in CpG sites with ≥10 reads in coverage and ≥25% methylation differences between normal and tumor tissues using the logistic regression method. DMRs were detected for regions containing ≥3 CpG sites and at least 1 DMC and with ≥30% absolute mean CpG methylation difference by using an eDMR package on R
Promoter DMRs, which were defined as regions within ±2000 bp from TSSs for Refseq transcripts, were extracted using bedtools 2.25.0 (bedtools.readthedocs.io).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing the results of DMRs between 3 normal liver tissues and 3 liver tumor tissues, and the distance of DMRs from closest gene calculated by bedtools.
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| Submission date |
Mar 05, 2018 |
| Last update date |
Apr 04, 2018 |
| Contact name |
Keiko Nohara |
| E-mail(s) |
keikon@nies.go.jp
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| Phone |
81-29-850-2500
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| Organization name |
National Institute for Environmental Studies
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| Department |
Center for Health and Environmental Risk Research
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| Street address |
16-2 Onogawa
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| City |
Tsukuba |
| ZIP/Postal code |
305-8506 |
| Country |
Japan |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE111420 |
The DNA methylation profile of liver tumors in C3H mice and identification of differentially methylated regions involved in the regulation of tumorigenic genes |
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| Relations |
| BioSample |
SAMN08636340 |
| SRA |
SRX3765505 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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