Blue:RNA-Seq Analyses:C1 hNuc 1000 Dataset

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Overview

  • C1 Run Summary:

File:20chips Samplelist.png

  • Primary Mapping/Analysis done by Rui using our pipeline
  • More in depth analysis by Rui

Average cDNA Yields Across Runs

File:20 C1 Runs cDNA Yields 2.png


  • Circled experiments represent the same batch of nuclei. There is little effect of freezing the nuclei in 10%DMSO or running the nuclei on a small chip rather than the medium chip. Global levels of cDNA were reduced with adding a nuclei stain/wash step to the loading protocol using the DNA Seq Cell Wash buffer. Also, addition of PolydIdC did globally increase cDNA levels even for the 0_Nuc conditions.
  • Examination of basic mapping stats shows that the small chip run 19 was highly variable (likely due to capture of small low RNA containing nuclei), while addition of PolydIdC seemed to stabilize mapping rates. Also, even though the cDNA yields were very high for the 0_Nuc with PolydIdC, most of the reads still mapped to ERCC.