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Status |
Public on Sep 18, 2023 |
Title |
GM12878_indexTag1_scWGS |
Sample type |
SRA |
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Source name |
Blood, Cell line
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Organism |
Homo sapiens |
Characteristics |
tissue: Blood, Cell line cell line: GM12878 cell type: Lymphoblastoid Cell Line
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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.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 2000 |
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Description |
RobustCNV.GM12878.tgz
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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
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Submission date |
Sep 18, 2023 |
Last update date |
Oct 16, 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 |
GPL30173 |
Series (1) |
GSE243430 |
Accessible high-throughput single-cell whole genome sequencing with paired chromatin accessibility |
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Relations |
BioSample |
SAMN37446104 |
SRA |
SRX21818728 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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