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Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming I

ABSTRACT: We collected single or duplicate samples at the various time points, generated single cell suspensions and performed scRNA-Seq. We also collected samples from established iPSC lines reprogrammed from the same MEFs, maintained in either 2i or serum conditions. Overall, we profiled 68,339 cells to an average depth of 38,462 reads per cell. After discarding cells with less than 1,000 genes detected, we retained a total of 65,781 cells, with a median of 2,398 genes and 7,387 unique transcripts per cell.

ORGANISM(S): Mus musculus

PROVIDER: GSE106340 | GEO | 2019/01/31

REPOSITORIES: GEO

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Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming II

Project description:We collected duplicate samples at the various time points, generated single cell suspensions and performed scRNA-Seq. We also collected samples from established iPSC lines reprogrammed from the same MEFs, maintained in either 2i or serum conditions. Overall, we profiled ~250,000 cells.

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Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming III

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Optimal transport analysis reveals trajectories in steady-state systems.

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Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-01-31 | GSE122662 | GEO

Single-cell RNA sequencing facilitates quantitative analysis of mouse hematopoietic stem/progenitor cells and SCF/2i expanded cells

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Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming.

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Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming

Project description:Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming

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An investigation into the effects of ATV:Trem2 on AD model mice using scRNA-seq

Project description:WT hTfR-KI mice and APP/SAA hTfR-KI mice were treated with one of: Isotype control ATV, naked 4D9 (activating Trem2 Ab), or ATV:4D9. Drugs were delivered IV. After 24 hours, mice were sacrificed, and perfused cortices were processed into single-cell suspensions. The suspensions were FACS sorted for Cd45+/Cd11b+ cells. Single-cell suspensions were labeled with CellPlex CMO per 10X Genomics protocol (CG000391 Rev A.) After each sample was labeled with CMO tags, equal numbers of cells per sample were combined into sample pools for single cell capture on the Chromium using Chromium Next GEM Single Cell 3’ v3.1 kit. After RT and cDNA amplification, each sample pool was separated into one gene expression (GE) library and one CMO tag library via dual-sided SPRI bead purification. Library preparation was performed per manufacturer’s protocol (CG000388 Rev A)

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