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Sample GSM4672467 Query DataSets for GSM4672467
Status Public on Dec 01, 2021
Title TAC 3 weeks biological replicate 1 RRBS
Sample type SRA
 
Source name Isolated cardiac myocytes
Organism Mus musculus
Characteristics treatment: TAC
time: 3 weeks
Treatment protocol DNA was isolated from mouse cardiomyocytes 3 days and 3 weeks after transverse aortic constriction (TAC) and CTCF depletion.
Growth protocol -
Extracted molecule genomic DNA
Extraction protocol DNA from left ventricular isolated adult cardiomyocytes was isolated using the QIAshredder kit (Qiagen).
Initial digestion into CpG rich regions was done by the Msp1 enzyme (NEB). The 3’ → 5’ Klenow exonuclease was used to repair sticky ends and promote poly-A tail synthesis. To facilitate multiplexing, individual TruSeq Illumina adapters were ligated to samples using the QIAseq Methyl Library Kit (Qiagen). Samples were then filtered to enrich for DNA fragments within the desired size range using magnetic AMPure XP beads (Beckman). Bisulfite conversion was performed using the Zymo EZ DNA Methylation-Lightning kit (Zymo).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina NovaSeq 6000
 
Data processing Single-end reads were demultiplexed into sample-specific *.fastq files using custom scripts and then aligned to the mouse genome using the BSseeker2 v2.0.10.
Briefly, we built an mm10-based reference index—simply 40-400bp MspI restriction fragments digested in silico and consistent with our enriched fragment size—using the bs_seeker2-build.py script.
We then aligned single-end reads to the reference index with bs_seeker2-align.py, using the 40-400bp fragment size range and -r flag to indicate RRBS libraries, and allowing up to 5 mismatches. We selected Bowtie2 as the aligner within BSseeker2 for this step.
Samtools was used to sort the resulting .bam files, and methylation was called using bs_seeker2-call_methylation.py, using a 10 read coverage minimum for any given cytosine, and removing all reads that did not undergo full bisulfite conversion.
From the resulting CGmaps, we retained cytosines that exist within a CpG (cytosine followed by guanine) context. These are deposited herein as processed data.
Genome_build: mm10
Supplementary_files_format_and_content: CGmap files
 
Submission date Jul 15, 2020
Last update date Dec 01, 2021
Contact name Tom Vondriska
E-mail(s) vondriska.web@gmail.com
Organization name UCLA
Street address 650 Charles E Young Dr, BH553
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL24247
Series (2)
GSE154520 Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RRBS]
GSE154521 Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation
Relations
BioSample SAMN15545636
SRA SRX8740605

Supplementary file Size Download File type/resource
GSM4672467_TAC3wks_rep1_RRBS.CGmap.gz 15.4 Mb (ftp)(http) CGMAP
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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