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µATACseq: ATACseq with as few as 100 cells

ABSTRACT: μATACseq data generated from 100, 500 and 1,000 FACS-purified Atoh1-GFP expressing cerebellar granule precursors (CGPs) are consistent with those from 20,000 CGPs by the standard ATACseq protocol (R > 0.85), with comparable percentages of both the reads mapped to the promoters (±1000bp Transcription Start Sites), and to the distal elements. Of the peaks identified from the standard ATACseq method, more than 70% are detected among those from the μATACseq with as low as 100 cells. In addition, μATACseq lowers the sequencing cost by generating 10-fold fewer mitochondrial reads and up to 1.7-fold fewer PCR duplicates. Surprisingly, the μATACseq protocol is robust over a 10-fold difference in the transposase-to-cell ratios measured by (1) the fragment size distribution inferred from pair-end sequencing, (2) the depth of the predicted transcription factor footprints, (3) and the concordance between biological replicates. Further more, μATACseq is fast and convenient, does not require multiple washing steps or nuclear isolation, and demands only 20 minutes prior to DNA purification and sequencing library amplification.

ORGANISM(S): Mus musculus

PROVIDER: GSE150275 | GEO | 2021/07/09

REPOSITORIES: GEO

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µATACseq: ATACseq with as few as 100 cells

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