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Status |
Public on Jan 17, 2018 |
Title |
Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells |
Organisms |
Mus musculus; synthetic construct |
Experiment type |
Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Methylation profiling by high throughput sequencing
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Summary |
Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report the first single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.
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Overall design |
scNMT-seq (single-cell nucleosome, methylation and transcription sequencing)
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Contributor(s) |
Clark S, Argelaguet R, Kapourani C, Stubbs T, Lee H, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni J, Stegle O, Reik W |
Citation(s) |
29472610 |
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Submission date |
Jan 16, 2018 |
Last update date |
Mar 25, 2019 |
Contact name |
Felix Krueger |
E-mail(s) |
fkrueger@altoslabs.com
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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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Platforms (4)
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GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
GPL15228 |
Illumina HiSeq 2000 (synthetic construct) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
GPL19424 |
Illumina NextSeq 500 (synthetic construct) |
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Samples (244)
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Relations |
BioProject |
PRJNA430259 |
SRA |
SRP131024 |