|
| Status |
Public on Mar 29, 2021 |
| Title |
Malaria_Patient_2_VDJ+GEX scRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral mononuclear blood cells (PBMCs)
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Malaria
age: 30 years
Sex: Female
tissue: Blood
|
| Growth protocol |
Peripheral blood draw was done, and mononuclear cells were isolated by ficoll gradient purification. B cells were isolated with the EasySep Human B cell isolation kit on a RoboSep platform
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were encapsulated in droplets using the Chromium Controller (10X Genomics). Reverse transcription and cDNA amplification were performed using the Chromium Single Cell 5’ kit (10X Genomics). All steps were done according to manufacturer’s instructions. 100 ng of cDNA (25% of generated cDNA) was used as input for library preparation.
Libraries were sequenced using the Illumina Hiseq3000 platform 8 lanes of sequencing at 26bp-8bp-98bp according to 10X Genomics sequencing recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
The sample replicates were split into 8 Hiseq 2500 sequencing anes and for each replicate, the lanes were merged into a single count matrix using Cell Ranger v3.0 (10X Genomics). Further, the resultant counts matrices for each replicate were processed using an inhouse single-cell RNA-seq pipeline that uses Seurat v 3.0
Genome_build: Human - hg38
Supplementary_files_format_and_content: CSV files are generated from CellrangerV3.0 and gene expression matrix is generated using SeuratV3.0. A VDJ sequences file is provided for each barcoded cell
|
| |
|
| Submission date |
Mar 29, 2021 |
| Last update date |
Mar 29, 2021 |
| Contact name |
Arun Boddapati |
| E-mail(s) |
[email protected]
|
| Organization name |
Yerkes National Primate research center
|
| Department |
Genomics Core
|
| Street address |
954 Gatewood Road, NE
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE149729 |
Chronic Malaria drives functional heterogenity in B cell subpopilations and expansion of unswitched atypical memory B cells |
| GSE157967 |
Shared transcriptional profiles at the single cell level of atypical memory B cells suggest common drivers of expansion and function in malaria, HIV and autoimmune diseases [Malaria VDJ+GEX scRNA-seq] |
|
| Relations |
| BioSample |
SAMN18528416 |
