mRNA Sequencing

T.Kouno, S.Kato, M.Mendez, I.Abugessaisa, J.Shin and C.Plessy
Division of Genomics Technologies, Center for Life Sciences Technologies, RIKEN, JAPAN

(...) Published on Rev B

  • supported ifcs:
    Open App IFC
  • number of ifc runs:


C1 CAGE is a method for single-cell transcriptome analysis for molecular counting of RNA 5'-ends. Paired-end sequencing, random priming and unique molecular identifiers are used for single-molecule fragment assembly of mRNAs and long non-coding RNAs, including non-polyadenylated transcripts. 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: C1 CAGEDuration (H:M): 12:00

Cell Load

Sample Prep

view protocol worksheet

Tested Primary Cells or Cell Lines

Cell Name Cell Type Source
HeLa Human cervix adenocarcinoma Cell line
A549 Human lung carcinoma Cell line


C1 CAGE uses random priming, unique moloecular identifier (UMI) and paired-end sequencing to allow molecular counting of mRNAs and lomg non-coding RNAs, including non-polyadenylated transcripts. In this method, 66.2% reads represent 5' ends of RNA in average. Amongst the 5' end reads, approximately 10% of rRNA, 15% of spike reads and 50% of genome mapped reads are represented. The UMI counts the number of RNA molecules per single cell. In average 8,000 molecules per single cell were detected by Miseq sequencer.

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