|
| Status |
Public on May 15, 2020 |
| Title |
scRNA Human Blood IFN lambda |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral Blood
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Healthy
tissue: Peripheral Blood
cell type: Immune cells
treatment: IFN lambda
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens were isolated and smashed through a 70uM sterile filter to obtain single cell suspensions. Red blood cells (RBCs) were lysed using ACK lysing buffer. Cells were resuspended in RPMI supplemented with 10% FBS and 1% Pen/Strep. For human samples, cells were isolated from whole blood of healthy volunteers using ErythroClear RBC depletion kit (STEMCELL). Cells were resuspended in RPMI supplemented with 10% FBS and 1% Pen/Strep. Cells were treated with recombinant interferon for 4 hours as indicated.
Isolated cells were encapsulated using microfluidics technology, and barcoded using a unique molecular identifier (UMI).
scRNAseq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
human_blood_ifnlambda
Healthy Donor Patient
Exp ID: 190723_0257_B4
Lab data ID: F4L
mRNA
read1_26/i7index_8/read2_98
|
| Data processing |
Raw sequencing data were processed with Cell Ranger software (version 3.0.2). Cell Ranger output files were loaded into R for analysis using the Seurat package. Low quality cells were removed based on % mitochondrial gene expression. Data were integrated, normalized, and transformed for downstream analysis. Clustering was performed using the UMAP algorithm. Cell clusters were annotated using the SingleR algorithm. Unclassified cells were removed from downstream analysis. Gene expression was subsequently determined in each cluster. Data were visualized using ggplot2.
Genome_build: Mouse: mm10 (GRCm38); Human: GRCh38
Supplementary_files_format_and_content: barcodes.tsv: Cell Ranger count raw_feature_bc_matrix barcodes.
Supplementary_files_format_and_content: features.tsv: Cell Ranger count raw_feature_bc_matrix features.
Supplementary_files_format_and_content: matrix.mtx: Cell Ranger count raw_feature_bc_matrix matrix.
|
| |
|
| Submission date |
Dec 26, 2019 |
| Last update date |
May 15, 2020 |
| Contact name |
Hong-wei Sun |
| Organization name |
NIAMS
|
| Department |
Office of Science & Technology
|
| Lab |
Biodata Mining & Discovery Section
|
| Street address |
9000 Rockville Pile
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE142637 |
Interferon lambda promotes immune dysregulation and tissue inflammation in TLR7-induced lupus [scRNA-seq] |
|
| Relations |
| BioSample |
SAMN13683683 |
| SRA |
SRX7443301 |
