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| Status |
Public on Feb 25, 2015 |
| Title |
CCE_EB_7d.1_3 |
| Sample type |
SRA |
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| Source name |
CCE
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| Organism |
Mus musculus |
| Characteristics |
cell line: CCE
treatment: EB
cell_number: 1 cell
replicate: 3
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| 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.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| 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>
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| Submission date |
Jan 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
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| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
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| Street address |
Lazarettgasse 14
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| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE65196 |
Single-cell DNA methylome sequencing and bioinformatic inference of epigenetic cell state dynamics |
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| Relations |
| BioSample |
SAMN03291053 |
| SRA |
SRX849983 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1589252_CCE_EB_7d.1_3.txt.gz |
2.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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