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| Status |
Public on Feb 08, 2023 |
| Title |
sciATACv3 nanowell-based preparation on mouse whole brain tissue |
| Sample type |
SRA |
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| Source name |
whole brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: whole brain
strain: C57BL6
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted by mincing tissue with a razor blade in ice cold using Nuclei Isolation Buffer (NIB) followed by dounce homogenization in NIB, then spinning down at 500xg, removing the supernatant and resuspending in NIB.
Single-cell combinatorial indexed ATAC-seq was performed by tagmenting nuclei in 96-well plates using uniquely barcoded tagmentaiton complexes followed by pooling tagmented nuclei from all wells, washing in NIB, then distributing nuclei to a 5,184 nanowell chip using the iCell8 instrument for indexed PCR amplificaiton, pooling, and sequencing.
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
accessible chromatin DNA
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| Data processing |
Barcode demultiplexing was performed using a 2-hamming distance match for each of the individual indexes followed by concatenation into a single error-corrected cell index read.
Reads were aligned to the mouse reference genome mm10 followed by rmeoval of duplicate reads, production of a frgaments bed file and loaded into ArchR
Assembly: mm10
Supplementary files format and content: ArchR Rds file containing fragments
Supplementary files format and content: Peaks called using macs2
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| Submission date |
Nov 28, 2022 |
| Last update date |
Feb 09, 2023 |
| Contact name |
Andrew Adey |
| E-mail(s) |
adey@ohsu.edu
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| Organization name |
Oregon Health & Science University
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| Department |
MMG
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| Lab |
Adey Lab
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| Street address |
3181 S.W. Sam Jackson Park Rd, RHH, L103
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| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239-3098 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE218881 |
Nanowell-based single-cell combinatorial indexed ATAC-seq |
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| Relations |
| BioSample |
SAMN31891392 |
| SRA |
SRX18397622 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6758138_sciATACv3.NV3.arrow |
53.6 Gb |
(ftp)(http) |
ARROW |
| GSM6758138_sciATACv3.NV3.bed.gz |
5.9 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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