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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 17, 2018 |
| Title |
ESC_B06_NOMe-seq |
| Sample type |
SRA |
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| Source name |
Embryonic stem cell NMT-seq
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| Organism |
Mus musculus |
| Characteristics |
cell line: El16 embyonic stem cell
strain: 129xCast/129
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| Growth protocol |
ESCs were cultured in serum/LIF conditions as described previously (Ficz et al., Cell Stem Cell 13, 351–359)
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| 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)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Single-cell methylation and accessibility data obtained using NOMe-seq
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| 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>
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| Submission date |
Jan 16, 2018 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Felix Krueger |
| E-mail(s) |
[email protected]
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| Organization name |
Altos Labs
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| Department |
Bioinformatics
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| Street address |
Granta Park
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| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE109262 |
Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells |
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| Relations |
| BioSample |
SAMN08368195 |
| SRA |
SRX3585615 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2936204_ESC_B06_CpG-met_processed.tsv.gz |
5.8 Mb |
(ftp)(http) |
TSV |
| GSM2936204_ESC_B06_GpC-acc_processed.tsv.gz |
44.7 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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