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Status |
Public on May 30, 2024 |
Title |
Healthy_female_11404_1_B025_ATAC |
Sample type |
SRA |
|
|
Source name |
peripheral blood mononuclear cells
|
Organism |
Homo sapiens |
Characteristics |
patient_id: 11404 patient_visit: 11404_1 disease: Healthy patient_age: 61 Sex: female days_symptom_onset: n/a draw_date: 2020-05-11 visit: Visit 1 sequencing_batch: B025 olink_sample_id: FSQHAZ0BH55-03
|
Extracted molecule |
genomic DNA |
Extraction protocol |
PBMCs were removed from liquid nitrogen storage and immediately thawed in a 37C water bath. Cells were diluted dropwise with 37°C AIM V media up to a final volume of 10 mL. A single wash was performed in 10 mL of PBS+BSA. PBMCs were resuspended 2 mL in PBS+BSA, counted on a ViCell or Cellometer Spectrum, as above, and 1x106 cells were incubated sequentially or together with Human Trustain FcX (BioLegend #422302) and Fixable Viability Stain 510 (BD #564406), on ice according to manufacturer’s instructions. Cell were washed with PBS+BSA and stained with a master mix cocktail of antibodies (STAR*Methods/Antibodies) on ice for 25-30 minutes Single-cell RNA-seq libraries were generated using the 10X Genomics Chromium 3’ Single Cell Gene Expression assay (#100075 or #1000121) and Chromium Controller Instrument according to the manufacturer’s published protocol. 16,000 cells from each PBMC sample was loaded into a separate Chromium Single Cell Chip B (10X Genomics #1000073) well targeting a recovery of 10,000 cells. Gel Beads-in-emulsion (GEMs) were then generated using the 10X Chromium Controller.
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger/cellranger-atac mkfastq (10x Genomics v.1.1.0). 10x cellranger/cellranger-atac count was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome (refdata-cellranger-atacGRCh38-1.1.0). The output files for rna: atac: fragments.tsv.gz and singlecell.csv were utilized for downstream processing and quality control analysis. HDF5 files (filtered) were then uploaded into R statistical programming language using the Seurat package (version 4.0) where normalization, scaling, integration and reference based label transfer was performed. Genome_build: Ensembl GRCh38-3.0.0 Supplementary_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 |
Apr 29, 2021 |
Last update date |
May 30, 2024 |
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 |
GPL27644 |
Series (1) |
GSE173590 |
Longitudinal trajectories of mild/moderate SARS-CoV2 infection reveals key precursors and predictors of convalescent virus-specific immunity |
|
Relations |
BioSample |
SAMN18926212 |