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

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 of population differentiation in gene expression at the single-cell level. Data from the mixture provides additional valuable information facilitating the development of statistical methods for data normalization and batch effect correction.

Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization

“…Moreover, studies of transcription reveal expression heterogeneity 32 . Also in the same cells that we studied-GM12878, heterogeneity was shown using single cell sequencing approaches -scATAC-Seq 33 and scRNA-Seq 34 when compared with bulk studies. It suggests that variability observed by us and others could interplay with transcriptional activity.…”

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

“…The sequencing data from this study have been submitted as the BioProject reference (PRJNA508890), with descriptions of the Biosamples (SUB4895416, SUB4895422, SUB4895423). Raw data of three samples have been deposited at the National Center for Biotechnology Information (NCBI) Sequence Reads Archive (SRA) with accession ID: SRP172838 36 . For each sample, data include unprocessed scRNA-seq reads in two raw fastq files (*R1.fastq.gz for cell barcodes and UMIs, and *R2.fastq.gz for RNA reads), as well as an expression matrix file in matrix market exchange format (*.mtx) with columns corresponding to cells and row to genes.…”

“…For each sample, data include unprocessed scRNA-seq reads in two raw fastq files (*R1.fastq.gz for cell barcodes and UMIs, and *R2.fastq.gz for RNA reads), as well as an expression matrix file in matrix market exchange format (*.mtx) with columns corresponding to cells and row to genes. UMI matrices of this study have been deposited with the Gene Expression Omnibus at GEO: GSE126321 37 . The identifiers for the columns and rows are included in separated files (barcodes.tsv and genes.tsv).…”

Extent, heritability, and functional relevance of single cell expression variability in highly homogeneous populations of human cells

“…We estimated single cell expression variability (scEV) individually. To obtain the scRNA-seq data for LCL, we cultured GM12878, an LCL strain widely used in genomic research, prepared cells using a 10X Genomics Chromium Controller, and sequenced a total of 7,045 cells (Osorio et al 2019). This data has been deposited in the NCBI GEO database (Accession number GSE126321, Data Availability).…”

“…To test this, we performed the scRNA-seq with another LCL-GM18502, derived from a donor of African ancestry, unrelated to GM12878. We processed GM18502 along with GM12878 in the same batch (Materials and Methods), along with a technical replicate sample made from a 1:1 mixture of the two (Osorio et al 2019). For comparison, we also obtained scRNA-seq data from the study of (Zhang et al 2019) for another LCL GM12981.…”