GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM6758138 Query DataSets for GSM6758138
Status Public on Feb 08, 2023
Title sciATACv3 nanowell-based preparation on mouse whole brain tissue
Sample type SRA
Source name whole brain
Organism Mus musculus
Characteristics tissue: whole brain
strain: C57BL6
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.
Library strategy ATAC-seq
Library source genomic single cell
Library selection other
Instrument model Illumina NovaSeq 6000
Description accessible chromatin DNA
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
Submission date Nov 28, 2022
Last update date Feb 09, 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
Platform ID GPL24247
Series (1)
GSE218881 Nanowell-based single-cell combinatorial indexed ATAC-seq
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap