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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 |
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Source name |
peripheral blood mononuclear cells
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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
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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.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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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
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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).
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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 |
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Platform ID |
GPL24676 |
Series (1) |
GSE158013 |
Simultaneous trimodal single cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq |
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Relations |
BioSample |
SAMN18105805 |