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Sample GSM2936211 Query DataSets for GSM2936211
Status Public on Jan 17, 2018
Title ESC_C04_NOMe-seq
Sample type SRA
 
Source name Embryonic stem cell NMT-seq
Organism Mus musculus
Characteristics cell line: El16 embyonic stem cell
strain: 129xCast/129
Growth protocol ESCs were cultured in serum/LIF conditions as described previously (Ficz et al., Cell Stem Cell 13, 351–359)
Extracted molecule genomic DNA
Extraction protocol DNA and mRNA were seperately purified from single cells using the G&T-seq protocol described previously (Macaulay et al., Nature Protocols, 2016)
Libraries were prepared using scBS-seq protocol described previously (Clark et al., Nature Protocols 2017)
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Description Single-cell methylation and accessibility data obtained using NOMe-seq
Data processing Libraries were sequenced on the Illumina HiSeq or NextSeq platform using the default RTA analysis software.
Raw sequence reads had the first 6 base pairs clipped off the 5' end to remove the 6N random priming portion of the reads, and were also trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.3, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 6). Remaining sequences were then aligned to the mouse genome (build GRCm38) with Bismark (v0.17.1) in single-end mode (parameters: --non_directional). Methylation calls were extracted after duplicate sequences had been excluded. Regions that were covered by a disproportionally high read number and were most likely mapping artefacts were excluded from subsequent analysis.
genome build: GRCm38
Supplementary_files_format_and_content: The genome-wide CpG/GpC methylation/accessibility reports are tab-delimited, use 1-based genomic coordinates Supplementary_files_format_and_content:: and are in the following format: <chromosome> <position> <methylation rate>
 
Submission date Jan 16, 2018
Last update date Jan 24, 2018
Contact name Felix Krueger
E-mail(s) fkrueger@altoslabs.com
Organization name Altos Labs
Department Bioinformatics
Street address Granta Park
City Cambridge
ZIP/Postal code CB21 6GP
Country United Kingdom
 
Platform ID GPL13112
Series (1)
GSE109262 Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells
Relations
BioSample SAMN08368086
SRA SRX3585622

Supplementary file Size Download File type/resource
GSM2936211_ESC_C04_CpG-met_processed.tsv.gz 6.1 Mb (ftp)(http) TSV
GSM2936211_ESC_C04_GpC-acc_processed.tsv.gz 49.3 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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