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Status |
Public on Mar 20, 2023 |
Title |
MeDIP of C5F1 no, sample 16_10 |
Sample type |
SRA |
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Source name |
normal intestinal mucosa
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 x CSS C57BL/6 chr5 PWD F1 genotype: APC min tissue: normal intestinal mucosa age: 15-19 weeks antibody: 5-methylcytosine
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was isolated using the Allprep DNA Mini Kit (Qiagen, Hilden, Germany), according to manufacturer´s protocols. Methyl-DNA enrichment was done according to Grimm C, Adjaye J (2012) Analysis of the methylome of human embryonic stem cells employing methylated DNA immunoprecipitation coupled to next-generation sequencing. Methods Mol Biol 873: 281–295. Library construction was done according to Grimm C, Adjaye J (2012) Analysis of the methylome of human embryonic stem cells employing methylated DNA immunoprecipitation coupled to next-generation sequencing. Methods Mol Biol 873: 281–295. Sequencing was performed on an Illumina Genome Analyser IIx.
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Library strategy |
MeDIP-Seq |
Library source |
genomic |
Library selection |
5-methylcytidine antibody |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
C5F1_no_MeDIP16_10 processed data file: modifiers_medipseq_counts_all.csv
|
Data processing |
Alignment of MeDIP-seq reads to the PWD(assembly)/B6(mm10) mixed reference using bwa. PWD reads are mapped to their corresponding position in the mm10 reference genome. Quantification of reads per window with qsea. Genome_build: mm10/PWD assembly version 2b Supplementary_files_format_and_content: modifiers_medipseq_counts_all.csv.gz: Comma-separated text file with the MeDIP counts per 250 base genomic window. Input samples have not been quantified.
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|
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Submission date |
Apr 09, 2020 |
Last update date |
Mar 20, 2023 |
Contact name |
Markus Morkel |
E-mail(s) |
markus.morkel@charite.de
|
Organization name |
Max Planck Institute for molecular Genetics
|
Street address |
Ihnestraße 63-73
|
City |
Berlin |
ZIP/Postal code |
14195 |
Country |
Germany |
|
|
Platform ID |
GPL11002 |
Series (2) |
GSE148369 |
Intestinal cancer modifier MeDIP-Seq |
GSE148370 |
PWD/Ph-encoded genetic variants suppress ApcMin-triggered intestinal tumor formation by modulating the cellular Wnt/beta-Catenin response |
|
Relations |
BioSample |
SAMN14567158 |
SRA |
SRX8089970 |