|
| Status |
Public on May 16, 2020 |
| Title |
PBMCs, Day_minus_1 |
| Sample type |
SRA |
| |
|
| Source name |
Sorted PBMC
|
| Organisms |
Homo sapiens; Dengue virus |
| Characteristics |
cell type: Pooled CD3+CD19- T cells and CD3-CD19+ B cells
infection: DENV infection
time: Fever day -1
|
| Treatment protocol |
Cryopreserved PBMCs were thawed and washed with RPMI media supplemented with 10% fetal calf serum prior to analysis. Populations of interest (CD3+CD19- T cells and CD3-CD19+ B cells) were isolated from the unfractionated PBMCs by flow cytometric sorting using a BD FACSAria Fusion instrument. Post-sort population purity was assessed prior to downstream analysis, and sorted T and B cells pooled together in for subsequent processing. Sorted cells were washed in PBS supplemented with 2% fetal calf serum prior to scRNAseq library generation
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell RNAseq libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) and the Chromium Single Cell Analyzer (10x Genomics) according to the manufacture's protocol (User guide RevC)
Indexed sequencing libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) according to the manufacture's protocol (User guide RevC). In short, sequencing libraries were generated by 1) transcript fragmentation and end-repair, 2) post-fragmentation size-selection using SPRIselect beads, 3) Adaptor ligation and 4) sample index PCR and SPRIselect cleanup
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v2.1.1 mkfastq pipline (10x Genomics) and bcl2fastq2 v 2.20.0 (Illumina)
Data qualty control, data filtering, cell barcode processing, UMI compression, 5' transcript alignment, and single-cell gene counting was performed using the CellRanger v2.1.1 count pipeline (10x Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv, mtx files generated by CellRanger v2.1.1
|
| |
|
| Submission date |
Mar 17, 2020 |
| Last update date |
May 17, 2020 |
| Contact name |
Adam Tully Waickman |
| Organization name |
SUNY Upstate Medical University
|
| Street address |
766 Irving Avenue
|
| City |
Syracuse |
| State/province |
New York |
| ZIP/Postal code |
13210 |
| Country |
USA |
| |
|
| Platform ID |
GPL28283 |
| Series (2) |
| GSE147104 |
Detection of DENV infected cells following natural dengue infection |
| GSE147110 |
Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq |
|
| Relations |
| BioSample |
SAMN14390957 |
| SRA |
SRX7925314 |
