|
| Status |
Public on Mar 20, 2023 |
| Title |
MeDIP of B6 wt, sample 4_5 |
| Sample type |
SRA |
| |
|
| Source name |
normal intestinal mucosa
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild type
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.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
B6_wt_MeDIP4_5
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.
|
| |
|
| 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 |
SAMN14567140 |
| SRA |
SRX8089999 |
