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| Status |
Public on Jun 04, 2020 |
| Title |
Allele-specific mRNA expression analysis in 129/CAST hybrid mESCs by single-cell full-length total RNA-sequencing |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Cell-to-cell heterogeneity in gene expression can even be observed in the same type of cells, present in a similar environment. Transcriptional bursting is thought to be one of contributing factors to the heterogeneity, but it remains elusive how the kinetic properties of transcriptional bursting (e.g. burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. Here, by using single-cell, full-length total RNA-sequencing, we performed genome-wide analysis of transcriptional bursting in mouse embryonic stem cells (mESCs). We found that the kinetics of transcriptional bursting is gene-specific and is determined by a combination of promoter and gene body binding proteins, including polycomb repressive complex 2 and transcription elongation-related factors.
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| Overall design |
To study kinetic properties of transcriptional bursting genome-wide, we analyzed allele-specific mRNA levels in 129/CAST hybrid mESCs (grown on Laminin-511 (LN511) without feeder cells in G1 phase) by RamDA-Seq - a highly sensitive RNA-Seq method capable of determining the full-length of transcript at single cell level (Hayashi et al., 2018).
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| Web link |
https://bit.riken.jp/
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| |
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| Contributor(s) |
Hayashi T, Nikaido I, Ochiai H |
| Citation(s) |
32596448 |
| |
| Submission date |
Jun 12, 2019 |
| Last update date |
Jul 15, 2020 |
| Contact name |
Itoshi NIKAIDO |
| E-mail(s) |
itoshi.nikaido@riken.jp
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| Organization name |
RIKEN
|
| Department |
Center for Biosystems Dynamics Research
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| Lab |
Laboratory for Bioinformatics Research
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| Street address |
2-1 Hirosawa
|
| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (419)
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| This SubSeries is part of SuperSeries: |
| GSE132593 |
Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells |
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| Relations |
| BioProject |
PRJNA548635 |
| SRA |
SRP201374 |
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