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Sample GSM4796271 Query DataSets for GSM4796271
Status Public on Feb 15, 2021
Title LCL_777_B958
Sample type SRA
Source name primary B cells (EBV-infected)
Organisms Homo sapiens; human gammaherpesvirus 4
Characteristics cell type: B lymphocyte
donor: 777
viral strain (transformant): B95-8
Treatment protocol No additional treatments were applied after primary cell infection and culture
Growth protocol Primary human B cells were isolated from whole blood by Ficoll gradient. CD19+ B cells were isolated from purified PBMCs by magnetic separation. Purified B cells were infected in bulk by incubation with viral supernatnants prepared from stimulated B95-8 Z-HT or M81 cells. Viral supernatants were incubated with primary B cells for 1 hr at 37 degrees C with 5% CO2. Cells were rinsed in 1x PBS after infection and cultured in RPMI 1640 media with 15% fetal calf serum (R15). Prior to single cell preparation, outgrown LCLs were cultured in RPMI 1640 media with 10% fetal calf serum (R10) supplemented with 2 mM L-glutamine, 100 U/mL penicillin, 100 ug/mL streptomycin, and 0.5 ug.mL cyclosporine A.
Extracted molecule total RNA
Extraction protocol Each of the three samples was prepared separetly using the 10x Genomics Chromium controller
Standard library construction as specified by the manufacturer's protocols (v2 chemistry)
capture and single-cell indexing of total polyA mRNA
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description total polyA mRNA (single cell, host and viral)
Data processing [base-calling] Illumina HiSeq 3000/4000
[alignment] cellranger v.2.0.0 (mkfastq); alignment was performed against the human genome (hg38) concatenated with the type 1 EBV genome (NC_007605) as an extra chromosome to capture viral transcripts
[qc filtering] Seurat v.3.1.5 (R); filtered out cells with <200 or >65000 unique RNA molecules and cells with >5% mitochondrial gene expression.
[normalization] Seurat v.3.1.5 (R)
[cell cycle marker regression] Seurat v.3.1.5 (R)
[scaling and feature selection] Seurat v.3.1.5 (R)
[PCA, dimensional reduction, and visualization] Seurat v.3.1.5 (R)
Supplementary_files_format_and_content: TSV, MTX
Submission date Sep 21, 2020
Last update date Feb 15, 2021
Contact name Elliott Daniel SoRelle
Organization name Duke University
Department Molecular Genetics & Microbiology
Lab Micah Luftig Lab
Street address 130 Research Drive (CARL Building)
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
Platform ID GPL23362
Series (1)
GSE158275 Single-cell characterization of transcriptomic heterogeneity in lymphoblastoid cell lines
BioSample SAMN16231004
SRA SRX9162428

Supplementary file Size Download File type/resource
GSM4796271_LCL_777_B958_UMI_barcodes.tsv.gz 8.5 Kb (ftp)(http) TSV
GSM4796271_LCL_777_B958_UMI_genes.tsv.gz 260.0 Kb (ftp)(http) TSV
GSM4796271_LCL_777_B958_UMI_matrix.mtx.gz 20.1 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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