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RNA-seq Process Controls

To monitor for consistent, high-quality sampling of single-cell and single-nucleus RNA-Seq data, eight controls (4 negative and 4 positive) were included in each Amplification set (8 controls + 88 samples). A control strip included 2 wells without cells (termed ERCC for External RNA Controls Consortium, negative), 2 wells without cells or ERCC (termed NTC for No Template Control, negative), 2 wells with 10 pg Control RNA (mouse) provided in the Takara SMART-Seq v4 kit (termed Control RNA, positive), and 2 wells with either 10 pg of Mouse Whole Brain Total RNA (termed MouseWhole, Zyagen MR-201, positive) or 10 pg of Human Universal Reference Total RNA (termed UHR, Takara 636538, positive). Controls for mouse and human data is available to download via the links below, and detailed methods are described in the Technical Whitepapers

Note that separate control sets are available for samples released in June 2018 and October 2018. 



Species Cortical Area Downloadable RNA-Seq data files
Human MTG

Controls Data | .gtf File

Human VISp, ACC

Controls Data | .gtf File

Mouse VISp, ALM

Controls Data | .gtf File

Mouse ACA, MOp (cells and nuclei)

Controls Data | .gtf File


Mouse Protocols  Human Protocols