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Sample GSM7785546 Query DataSets for GSM7785546
Status Public on Sep 18, 2023
Title GM12878_indexTag1_scWGS
Sample type SRA
 
Source name Blood, Cell line
Organism Homo sapiens
Characteristics tissue: Blood, Cell line
cell line: GM12878
cell type: Lymphoblastoid Cell Line
Extracted molecule genomic DNA
Extraction protocol Nuclei were extracted using NIB-Hepes buffer
Nuclei for scATAC and dTag were carried through tagmentation, dTag nuclei or nuclei for scWGS alone were carried through nucleosome disruption followed by tagmentation. dTag amnd multiplexed scWGS samples used indexed tagmentation using reagents from the ScaleBio scATAC multiplexing kit. Single-plex experiments used the tagmnetaiton enzyme provided in the 10x Genomics scATAC kit. After final tagmentation, nuclei were carried through the 10x scATAC v2 protocol according to the default protocol or using the modifications indicated by ScaleBio for samples that leevraged indexed tagmentation.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Description RobustCNV.GM12878.tgz
Data processing Reads were demultiplexed using unidex (github.com/adeylab/unidex), changing the read name to be the error-corrected cell barcode
Alignment was performed using bwa mem
Duplicate reads were removed on a cell-by-cell basis
Fragment files were generated using sinto (ATAC), or reads were tallied for each cell over tiling genomic windows (WGS)
WGS data were processed using RobustCNV and ATAC data using ArchR
Assembly: hg38
Supplementary files format and content: Gzipped fragment files are provided for all ATAC data
Supplementary files format and content: RobustCNV outputs of window biases and copy number calls in gzipped tar files
 
Submission date Sep 18, 2023
Last update date Oct 16, 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
 
Platform ID GPL30173
Series (1)
GSE243430 Accessible high-throughput single-cell whole genome sequencing with paired chromatin accessibility
Relations
BioSample SAMN37446104
SRA SRX21818728

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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