LPS Simulation and mRNA Seq

Cell Stimulation

Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, et al.
Regev, Park and May, Broad Institute, Harvard University, MIT, Hebrew University, Fluidigm Corporation

(...) Published on Rev B

  • supported ifcs:
    Open App IFC, mRNA Seq IFC
  • number of ifc runs:


Cells are loaded, stimulated with LPS, and incubated in-chip in a tissue culture incubator. After incubation, the cells are washed, lysed, reverse transcribed and amplified using Clontech SMARTer Ultra Low RNA Kit. This script has been updated to be compatible with all versions of the C1 Open App IFCs, including the redesigned medium 96 cell IFC.

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Protocol: LPS SimulationDuration (H:M): 4:00

Cell Load and Stimulation

Sample Prep

view protocol worksheet

Tested Primary Cells or Cell Lines

Cell Name Cell Type Source
Bone marrow derived dendritic cells Dendritic cells Primary


Stimulated 1,775 single dendritic cells, at various time courses for three pathogenic components (LPS, PIC (viral-like double-stranded RNA), and PAM (synthetic mimic of bacterial lipopeptides)) and additional perturbations. For most conditions, we captured up to 96 cells, and generated a matching population control. We sequenced each sample to an average depth of 4.5 +/- 3.0 million read pairs, as single-cell expression estimates stabilized at low read-depths.

Publications or Articles

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