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Sample GSM4417214 Query DataSets for GSM4417214
Status Public on May 16, 2020
Title PBMCs, Day_minus_2
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 -2
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 SAMN14390958
SRA SRX7925313

Supplementary file Size Download File type/resource
GSM4417214_Sample1_barcodes.tsv.gz 8.5 Kb (ftp)(http) TSV
GSM4417214_Sample1_genes.tsv.gz 258.6 Kb (ftp)(http) TSV
GSM4417214_Sample1_matrix.mtx.gz 10.1 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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