|
| Status |
Public on May 30, 2024 |
| Title |
Healthy_male_11558_1_B025_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
patient_id: 11558
patient_visit: 11558_1
disease: Healthy
patient_age: 77
Sex: male
days_symptom_onset: n/a
draw_date: 2020-06-24
visit: Visit 1
sequencing_batch: B025
olink_sample_id: FSQJAZ0BP8L-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.
|
| |
|
| 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).
|
| |
|
| 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 |
SAMN18926373 |
