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Series GSE218881 Query DataSets for GSE218881
Status Public on Feb 08, 2023
Title Nanowell-based single-cell combinatorial indexed ATAC-seq
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Here we present advancements in single-cell combinatorial indexed ATAC-seq (sciATAC) to measure chromatin accessibility that leverage nanowell chips to achieve atlas-scale cell throughput (>105) at low cost. Our optimized techniques also achieve a high fraction of reads that fall within called peaks (>80%) and low cell doublet rates. We also demonstrate an alternative workflow that achieves high cell coverage while retaining exceptional enrichment for open chromatin regions, enabling the assessment of >70,000 unique accessible loci per cell.
Overall design Single-cell combinatorial indexed ATAC-seq using nanowell-based compartmentalization for the second tier of cell indexing (PCR)
Contributor(s) Adey A, O'Connell B
Citation(s) 36792372
Submission date Nov 28, 2022
Last update date May 02, 2023
Contact name Andrew Adey
Organization name Oregon Health & Science University
Department MMG
Lab Adey Lab
Street address 3181 S.W. Sam Jackson Park Rd, RHH, L103
City Portland
State/province OR
ZIP/Postal code 97239-3098
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (3)
GSM6758136 sciATACv1 nanowell-based preparation on mouse whole brain tissue
GSM6758137 sciATACv2 nanowell-based preparation on mouse whole brain tissue
GSM6758138 sciATACv3 nanowell-based preparation on mouse whole brain tissue
BioProject PRJNA906077
SRA SRP410229

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Supplementary file Size Download File type/resource
GSE218881_RAW.tar 98.8 Gb (http)(custom) TAR (of ARROW, BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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