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Sample GSM1589207 Query DataSets for GSM1589207
Status Public on Feb 25, 2015
Title CCE.1_1
Sample type SRA
 
Source name CCE
Organism Mus musculus
Characteristics cell line: CCE
treatment: none
cell_number: 1 cell
replicate: 1
Extracted molecule genomic DNA
Extraction protocol Direct extraction of DNA following the steps of the EZ DNA methylation Direct Kit as described in the methods section in Farlik et al.
A novel method to perform library preparation from single cells as described in the methods section of Farlik et al.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Data processing Sequencing was performed on the Illumina HiSeq 2000 system using the standard 100bp paired-end configuration.
Raw sequence reads were trimmed using Trimmomatic (Bolger et al., 2014) version 0.32 with the following parameters: HEADCROP:6 ILLUMINACLIP:<Illumina_adapter_file>:2:10:4:1:true SLIDINGWINDOW:4:1 MAXINFO:16:0.40 MINLEN:16)
Trimmed reads were aligned against the human genome (hg19/GRCh37) and/or the mouse genome (mm10/GRCm38) using the Bismark Bisulfite Mapper (Krueger and Andrews 2011), version v0.12.2, parameter: –bowtie2). Duplicate reads were discarded and DNA methylation calls were extracted.
Reads containing fewer than three cytosines outside a CpG context that have been converted to thymines were discarded, which effectively removes unconverted and contaminating DNA fragments.
Genome_build: hg19/GRCh37 - mm10/GRCm38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: The genome-wide CpG methylation report is tab-delimited, uses 1-based genomic coordinates and is in the following format: <chromosome> <position> <strand> <count methylated> <count non-methylated> <C-context> <trinucleotide context>
 
Submission date Jan 22, 2015
Last update date May 15, 2019
Contact name Christoph Bock
E-mail(s) cbock@cemm.oeaw.ac.at
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL13112
Series (1)
GSE65196 Single-cell DNA methylome sequencing and bioinformatic inference of epigenetic cell state dynamics
Relations
BioSample SAMN03291105
SRA SRX849938

Supplementary file Size Download File type/resource
GSM1589207_CCE.1_1.txt.gz 9.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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