Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing
Summary
We performed single-cell transcriptome analysis (using MARS-seq) of mouse embryonic stem cells, embryiod bodies and mouse embryos. Additionally, we performed methylation analysis of bulk and single cells of this source (using whole-genome PBAT and PBAT capture).
Overall design
The ESCs lines that were used are J1 (SCRC1010, ATCC), Dnmt3a-/- clone 6aa, Dnmt3b-/- clone 8bb, Dnmt1-/- Dnmt3a -/- Dnmt3b-/- clone 19 (TKO) (Cell Bank Riken BioResource Research Center) , Dnmt3a -/- Dnmt3b-/- clones 7aabb and 16aabb (DKO) (kindly provided by Dr. Masaki Okano), Wild type, Dnmt3a and Dnmt3b knockout ES line, passages 3 or 5 in 2i/L, respectively (N15, kindly provided by Dr. Masaki Yagi). Embryiod bodies were generated by hanging drop protocol . Cells and embryos were collected dissociated and FACS-sorted into single-cell methylation or scRNA profiling or were collected as a bulk a long time points.
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