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| Status |
Public on Jun 03, 2024 |
| Title |
whole blood, scBS-6, scBS-seq |
| Sample type |
SRA |
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| Source name |
whole blood
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| Organism |
Mus musculus |
| Characteristics |
tissue: whole blood
genotype: wild type
cell type: whole blood depleted of red blood cells
genotype: wildtype
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
scM&T-seq (Angermueller et al 2016, https://doi.org/10.1038/nmeth.3728)
scBS-seq (Clark et al 2017, https://doi.org/10.1038/nprot.2016.187)
scBS-seq
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Sample 5503
sample5498-5505_processed_cov.tar.gz
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| Data processing |
scM&T-seq data was processed as described previously (Angermueller et al. 2016). scBS-seq data was processed as described previously; briefly, reads had 6bp removed on their 5’-ends to remove the random primed portion of the reads, and were also adapter- and quality-trimmed using Trim Galore (v0.6.7; options --clip_r1 6). Trimmed reads were aligned to the bisulfite converted GRCm38 mouse genome using Bismark v0.22.3 in single-end mode (Krueger and Andrews, 2011; options: --non_directional). Methylation calls were extracted after duplicate reads had been removed (deduplicate_bismark).
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files are tab separated and contain DNA methylation data with the following columns: chromosome, start, end, methylation, methylated reads, nonmethylated reads.
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| Submission date |
Feb 13, 2023 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Laura Biggins |
| E-mail(s) |
laura.biggins@babraham.ac.uk
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| Organization name |
The Babraham Institute
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| Department |
Bioinformatics
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| Street address |
Babraham Research Campus
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| City |
Cambridge |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE225171 |
Predicting age in single cells and low coverage DNA methylation data [scBS] |
| GSE225173 |
Predicting age in single cells and low coverage DNA methylation data |
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| Relations |
| BioSample |
SAMN33271418 |
| SRA |
SRX19354236 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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