|
| 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.
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| |
|
| Overall design |
Single-cell combinatorial indexed ATAC-seq using nanowell-based compartmentalization for the second tier of cell indexing (PCR)
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| |
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| 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 |
| E-mail(s) |
adey@ohsu.edu
|
| 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 |
| |
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| 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 |
|
| Relations |
| BioProject |
PRJNA906077 |
| SRA |
SRP410229 |
