Multi-modal single-cell sequencing of differentiating mESCs using Smart-seq3 and scATAC-seq

ABSTRACT: We report dynamics of X-chromosome upregulation (XCU) along X-chromosome inactivation (XCI) in mESCs as they differentiate into EpiSCs. F1 hybrid C57BL6/J × CAST/EiJ male and female mESCs were grown in serum/LIF conditions were differentiated using Fgf2 and Activin A for 1, 2, 4 and 7 days to induce random XCI in female cells. Multi-modal single-cell sequencing was performed using scATAC on nuclei and Smart-seq3 to assay chromatin accessibility and poly-A+ RNA expression, respectively. Allelic resolution is achieved using strain-specific SNPs in the data. We reveal dynamic balancing of X alleles as cells undergo XCI to compensate dosage imbalances between sexes as well as between X and autosomes. Furthermore, we reveal that female naïve mESCs with two active X chromosomes lack XCU on both

INSTRUMENT(S): Eppendorf EpMotion 5073m pipetting robot, NextSeq 550, Sony SH800

ORGANISM(S): Mus musculus

SUBMITTER: Antonio Lentini 

PROVIDER: E-MTAB-10714 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress