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Sample GSM1015972 Query DataSets for GSM1015972
Status Public on May 01, 2013
Title Single cell #4
Sample type SRA
Source name Mouse liver single cell
Organism Mus musculus
Characteristics tissue: liver
strain: C57BL/6
Treatment protocol Liver tissue was perfused with collagenase
Growth protocol C57BL/6 mice were obtained from the National Institute of Aging (NIA) and liver cells were collected and sequenced without growth
Extracted molecule genomic DNA
Extraction protocol Single hepatocytes were collected using hand-held capillaries under an inverted microscope
Library construction for RRBS sequencing was done as described by Meissner 2005 (PubMed: PMC1258174), but with MseI as digest vector and add adding 2 ng salmon DNA (samples H1,H2) or 2 ng tRNA cDNA (samples H3,H4) as buffer DNA to stabilize single-cell samples.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Description H4
Reduced Representation BS-Seq (RRBS)
Data processing Library strategy: RRBS-Seq
Basecalls were performed using CASAVA version 1.4
BS-Seq reads were preprocessed for better alignment quality using FASTX-toolkit 0.0.13, trimgalore 0.2.2 and cutadapt 1.0
BS-Seq reads were aligned to the mm10 genome using Bowtie2 2.0.0 and Bismark 0.7.6
CpG-Methylation calling was done using Bismark 0.7.6
CpG sites were grouped into regions of 1000 nt's with a minimum coverage of 10 CG sites using R 2.13 with custom scripts
Methylation status and differential methylation between single-cells and reference H1 were assessed using bayesian estimation for a beta-binomial model using R 2.13
Methylating epimutations were called on regions showing low methylation in the reference L1 but high methylation in a single-cell sample using R 2.13
Demethylating epimutations were called on regions showing high methylation in the reference L1 but low methylation in a single-cell sample using R 2.13
Genome_build: mm10
Supplementary_files_format_and_content: GFF listing all regions with methylation and demethylating epimutation were generated using R 2.13
Supplementary_files_format_and_content: GFF scores represent the CG methylation level of each region with epimutations
Submission date Oct 05, 2012
Last update date May 15, 2019
Contact name Kemal Akman
Phone +492215062161
Fax +492215062163
Organization name Max Planck Institute Cologne
Department Plant Breeding Research
Lab Tresch Group
Street address Carl-von-Linné-Weg 10
City Cologne
ZIP/Postal code 50829
Country Germany
Platform ID GPL13112
Series (1)
GSE41379 Single-cell DNA methylation analysis of epimutations in mouse liver cells.
SRA SRX192134
BioSample SAMN01758882

Supplementary file Size Download File type/resource
GSM1015972_H4.bin.demethEvents.gff3.gz 906 b (ftp)(http) GFF3
GSM1015972_H4.bin.methEvents.gff3.gz 241 b (ftp)(http) GFF3
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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