NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7433409 Query DataSets for GSM7433409
Status Public on May 31, 2023
Title Colon, 15 Months, Rep9
Sample type SRA
 
Source name Colon
Organism Mus musculus
Characteristics tissue: Colon
strain: C57BL/6J/Ukj
Sex: Male
age: 15 Months
Growth protocol All the mice were kept solely for aging in a controlled environment and health status.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen).
200 ng of DNA was fragmented via a 5 hour Msp1-digest (New England Biolabs), followed by TrueSeq adapter ligation (Illumina, San Diego, CA, USA) and subsequent bisulfite conversion following the manufacturers protocol (EZ DNA Methylation Gold Kit, Zymo Research). The bisulfite converted DNA was amplified in a 19-cycles PCR with Pfu Turbo Cx Hotstart DNA Polymerase (Agilent Technologies) and the resulting libraries were quality checked using 4200 TapeStation (Agilent Technologies). For sequencing of validation samples, Illumina’s next-generation sequencing methodology 87 was used. In detail, genomic DNA was quality checked and quantified using the 4200 TapeStation instruments in combination with the Genomic DNA ScreenTape (both Agilent Technologies). Libraries were prepared from 100 ng of input material using Ovation RRBS Methyl-Seq with TrueMethyl oxBS (Tecan). In detail, only the bisulfite part of the protocol was followed, oxidation of DNA was not done, and samples were treated as MOCK oxBS samples according to the manufacturer’s instruction. Quantification and quality check of libraries were done using the 4200 TapeStation and D5000 ScreenTapes instruments (both Agilent Technologies).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina NovaSeq 6000
 
Description 15M.N9
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz
Data processing Sequence information was converted to fastq format using bcl2fastq v2.20.0.422. From validation samples only those reads were downstream processed, that start with a Tecan/NuGen TrueMethyl diversity adapter (length 0-3, clipped afterwards) followed by a MspI cutting site.
Read quality trimming (cutoff 20) and TruSeq universal adapter clipping was performed using Cutadapt v2.10. Due to MspI cutting site end-repair, R1 adapter was prefixed by NN and in case of paired-end data, unconditional 5' clipping of length 2 was conducted on R2.
Mappings were done via segemehl v0.3.4 (methyl-C mode, accuracy 95%, reference GRCm38) and filtered for unique alignments. Paired-end alignments were further filtered for proper-read pairs and overlaps of R2 with R1 were trimmed using BamUtil clipOverlap v1.0.14.
Validation data alignments were deduplicated for over amplified PCR fragments based on unique molecular identifiers utilizing UMI-tools v1.1.1.
Methylation rates were inferred utilizing haarz v0.3.0. Rates and coverages within a CpG context were compiled using BEDTools v2.30.0.
Assembly: mm10
Supplementary files format and content: Tabular delimited text files in bedg format of read alignment coverages and inferred methylation rates per GRCh38 chromosomal CpG and sample.
 
Submission date May 30, 2023
Last update date May 31, 2023
Contact name Konstantin Riege
E-mail(s) konstantin.riege@leibniz-fli.de
Organization name Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Street address Beutenbergstraße 11
City Jena
ZIP/Postal code 07745
Country Germany
 
Platform ID GPL24247
Series (1)
GSE233734 Nonlinear DNA methylation trajectories in aging mice [RRBS]
Relations
BioSample SAMN35532025
SRA SRX20542047

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap