Single-cell RNA sequencing of a European and an African lymphoblastoid cell line

Daniel Osorio, Xue Yu, Peng Yu, Erchin Serpedin, James J. Cai

Research output: Contribution to journalArticle

Abstract

In biomedical research, lymphoblastoid cell lines (LCLs), often established by in vitro infection of resting B cells with Epstein-Barr virus, are commonly used as surrogates for peripheral blood lymphocytes. Genomic and transcriptomic information on LCLs has been used to study the impact of genetic variation on gene expression in humans. Here we present single-cell RNA sequencing (scRNA-seq) data on GM12878 and GM18502-two LCLs derived from the blood of female donors of European and African ancestry, respectively. Cells from three samples (the two LCLs and a 1:1 mixture of the two) were prepared separately using a 10x Genomics Chromium Controller and deeply sequenced. The final dataset contained 7,045 cells from GM12878, 5,189 from GM18502, and 5,820 from the mixture, offering valuable information on single-cell gene expression in highly homogenous cell populations. This dataset is a suitable reference for population differentiation in gene expression at the single-cell level. Data from the mixture provide additional valuable information facilitating the development of statistical methods for data normalization and batch effect correction.

Original languageEnglish
Number of pages1
JournalScientific data
Volume6
Issue number1
DOIs
Publication statusPublished - 4 Jul 2019

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RNA
Gene expression
Sequencing
Cells
Line
Cell
Blood
Lymphocytes
normalization
statistical method
Viruses
Gene Expression
Chromium
Statistical methods
Controllers
Genomics
Africa
Cell line
Genetic Variation
B Cells

ASJC Scopus subject areas

  • Statistics and Probability
  • Information Systems
  • Education
  • Computer Science Applications
  • Statistics, Probability and Uncertainty
  • Library and Information Sciences

Cite this

Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. / Osorio, Daniel; Yu, Xue; Yu, Peng; Serpedin, Erchin; Cai, James J.

In: Scientific data, Vol. 6, No. 1, 04.07.2019.

Research output: Contribution to journalArticle

Osorio, Daniel ; Yu, Xue ; Yu, Peng ; Serpedin, Erchin ; Cai, James J. / Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. In: Scientific data. 2019 ; Vol. 6, No. 1.
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