The BD Rhapsody™ ATAC-Seq Assays enable you to either generate highly reproducible open chromatin profiling data from single cells or perform a multiomic analysis of open chromatin accessibility and transcriptome of single cells in one experiment using the BD Rhapsody™ Single-Cell Analysis System.
Start here for a filtered table containing only ATAC-Seq FAQ. Easily searchable with CMD+F on a Mac or CTRL+F on a PC.
| Can I do a targeted mRNA assay with ATAC-seq? | You can only do a whole transcriptome assay(WTA) with the ATAC-seq workflow. |
| Are there any special considerations for using the Illumina NextSeq 2000 with BD Rhapsody ATAC-Seq libraries? | Although we haven't sequenced our libraries on the NextSeq 2000 platform, as long as the R1,R2 and index reads (containing cell label), can be generated, the bioinformatics pipeline will accept it. |
| Can I sequence ATAC-Seq libraries shorter than 50 bp for R1 and R2? | We did not do an extensive analysis with different read lengths to show its impact on ATAC-Seq data. So going shorter in read length would be at your own risk. That being said, our analysis pipeline supports reads as short as 30 bp for R1 and R2 of ATAC. |
| Can I use the RNAse inhibitor provided by BD as a part of the ATAC-Seq kit for nuclei isolation upstream of the BD ATAC+mRNA assay? | The RNAse inhibitor included as a part of the BD Rhapsody™ Multiomic ATAC-Seq Amplification Kit(571361) should not be used upstream of the workflow for nuclei preparation as the quantity is not sufficient. We recommend buying additional RNAse inhibitor from BD Biosciences on this link. You could also buy RNAse inhibitor from our recommended 3rd party vendors NEB and Watchmaker Genomics. See our nuclei prep protocols for details. |
| How many samples can I multiplex with the BD ATAC standalone or the Multiomic ATAC+mRNA assay? | Up to 6 different nuclei samples can be multiplexed at a time with the BD standalone ATAC or the Multiomic ATAC+mRNA assay. |
| How many nuclei can I run per lane of the cartridge with the BD Rhapsody ATAC standalone or the Multiomic ATAC+mRNA assay? |
The BD Rhapsody ATAC standalone or the Multiomic ATAC+mRNA assay has been validated for a maximum of 50k nuclei per lane. We have not tested higher than 50K nuclei with our assay. If you decide to try it at own risk, we would recommend scaling up the tagmentation reaction proportionately i.e. if 50ul of the reaction has has 50k nuclei, then for 70k nuclei you would need 70ul of total reaction volume. |
For Research Use Only. Not for use in diagnostic or therapeutic procedures.
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