Title: Single-cell ATAC-seq control of cross-contaminations (experiment 2)

Type Dataset Plessy, Charles, Kato, Sachi (2017): Single-cell ATAC-seq control of cross-contaminations (experiment 2). Zenodo. Dataset. https://zenodo.org/record/263695

Authors: Plessy, Charles (RIKEN Center for Life Science Technologies) ; Kato, Sachi (RIKEN Center for Life Science Technologies) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

On the Fluidigm C1 platform for single-cell analysis, the cells are captured in 96 chambers arranged serially, and then washed before further processing.  Thus, debris present from the loading medium or released by captured cells upstream are a possible source of contamination.  We generated a control datasets using the single-cell ATAC-seq protocol available from Fluidigm's ScriptHub.  We cultivated human Hep G2 and mouse Hepa 1-6 (both are liver cancer cell lines), stained them with green and red calceins (respectively), and loaded them at equal concentration in a Fluidigm medium flow cell (old design), before running the C1 single-cell ATAC-seq program. To evaluate damage and carry-over of debris from FACS-sorting, two IFCs were run in two C1 machines in parallel.  In the first (flowcell ID 1772-123-155), the cells not washed and in the second, they were washed (ID 1772-123-158).

The data deposited here is a sequencing run (Illumina MiSeq) of these ATAC-seq libraries. The metadata indicating the contents of each well is being uploaded separately and this record will be updated once the DOIs are available.

More information

• DOI: 10.5281/zenodo.263695

Subjects

• MiSeq, ATAC-seq, Fluidigm C1, single-cell

Dates

• Publication date: 2017
• Issued: January 30, 2017

Rights

• https://creativecommons.org/publicdomain/zero/1.0/legalcode Creative Commons Zero v1.0 Universal
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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