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Sample GSM5123950 Query DataSets for GSM5123950
Status Public on Apr 02, 2021
Title Multiome RNA/ATAC of leukapheresis-purified, 0.01% digitonin perm, FACS neutrophil-depleted PBMCs, method comparison
Sample type SRA
 
Source name peripheral blood mononuclear cells
Organism Homo sapiens
Characteristics donor_id: HMN200910
donor_source: BioIVT
purification_type: leukapheresis
preparation_type: permeabilized cells
preparation_conditions: 0.01% digitonin
cleanup_type: FACS
cleanup_conditions: Dead Cell/Debris/Neutrophil Depletion
library_type: 10x Multiome
library_type: 10x Multiome
Extracted molecule genomic DNA
Extraction protocol Biological specimens were purchased from BioIVT as cryopreserved PBMCs. All sample collections were conducted by BioIVT under IRB-approved protocols, and all donors sign informed consent forms. PBMCs sourced from BioIVT were isolated using leukapheresis. Following isolation, PBMCs were subjected to RBC lysis, washing, and counting. PBMC aliquots were cryopreserved in Cryostor CS10 (StemCell Technologies, 07930) and stored in vapor phase liquid nitrogen.
Unstained FACS sorted PBMCs were used as input to Nuclei and permeabilized cell Multiome ATAC plus Gene Expression library preparation. Nuclei were isolated according to 10x Genomics Demonstrated Protocol CG000365 Rev A exactly as recommended for cryopreserved PBMCs. Cells were permeabilized using 0.01% digitonin. Libraries were prepared according to the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC plus Gene Expression user guide CG000338 Rev A.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description X066-MP0C1W2_leukopak_perm-cells_multiome_200M_atac_filtered_fragments.tsv.gz
X066-MP0C1W2_leukopak_perm-cells_multiome_200M_atac_filtered_metadata.csv.gz
X066-MP0C1W2_leukopak_perm-cells_multiome_200M_cellranger-arc_filtered_feature_bc_matrix.h5
X066-MP0C1W2_leukopak_perm-cells_multiome_200M_cellranger-arc_per_barcode_metrics.csv.gz
X066-MP0C1W2
The FASTQs are from human subjects and will be provided via dbGAP
OTHER: 10x Genomics Multiome ATAC + RNA-Seq
Data processing Demultiplexing of raw base call files into FASTQ files was performed using bcl2fastq2 (Illumina v2.20.0.422
To perform comparisons between methodologies, all scRNA-seq and scATAC-seq libraries were downsampled to 200 million FASTQ entries (200M of each sequenced read; ~20,000 reads per expected cell recovered at ~10,000 cell expected recovery). 10x Multiome RNA and ATAC libraries were aligned using cellranger-arc software (v1.0.0, 10x Genomics) against 10x genomics reference refdata-cellranger-arc-GRCh38-2020-A using default parameters.
genome_build: Ensembl GRCh38-3.0.0
processed_data_files_format_and_content: Fragment TSVs (Tab separated), Single cell CSVs (Commas separated), and HDF5 file (Hierarchical Data Format).
 
Submission date Mar 02, 2021
Last update date Apr 02, 2021
Contact name Allen Institute For Immunology
E-mail(s) xiaojun.li@alleninstitute.org
Phone 2065487135
Organization name Allen Institute
Street address 615 Westlake Ave N, Seattle, WA
City Seattle
State/province Washington
ZIP/Postal code 98109
Country USA
 
Platform ID GPL24676
Series (1)
GSE158013 Simultaneous trimodal single cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq
Relations
BioSample SAMN18105805

Supplementary file Size Download File type/resource
GSM5123950_X066-MP0C1W2_leukopak_perm-cells_multiome_200M_atac_filtered_fragments.tsv.gz 412.6 Mb (ftp)(http) TSV
GSM5123950_X066-MP0C1W2_leukopak_perm-cells_multiome_200M_atac_filtered_metadata.csv.gz 712.7 Kb (ftp)(http) CSV
GSM5123950_X066-MP0C1W2_leukopak_perm-cells_multiome_200M_cellranger-arc_filtered_feature_bc_matrix.h5 60.4 Mb (ftp)(http) H5
GSM5123950_X066-MP0C1W2_leukopak_perm-cells_multiome_200M_cellranger-arc_per_barcode_metrics.csv.gz 21.2 Mb (ftp)(http) CSV
Processed data provided as supplementary file
Raw data not provided for this record

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