Single-Cell RNA-Seq GM12878 - SRA

SRX5235025: Single-Cell RNA-Seq GM12878
1 ILLUMINA (Illumina NovaSeq 6000) run: 474.4M spots, 142.3G bases, 50.8Gb downloads

Design: Lymphoblastoid cell lines obtained from the Coriell Cell Repositories were established by Epstein-Barr Virus (EBV) transformation of peripheral blood mononuclear cells using phytohemagglutinin as a mitogen. Cells were cultured in the recommended Roswell Park Memorial Institute (RPMI) Medium 1640 supplemented with 2mM L-glutamine and 20% of fetal bovine serum on T25 tissue culture flask with 20 mL medium upright position at 37C under 5% carbon dioxide. Lymphoblast cultures where split every four days to yield a cell density of 400,000 - 600,000 viable cells/mL. Suspended cells were pelleted by centrifugation in PBS (400g, 10min, 4C), the supernatant was discarded, and the pellet was resuspended in 1mL ice-cold PBS. Cell numbers and viability were assessed by Trypan blue staining and counting in a Neubauer improved counting chamber. Libraries were prepared using the Chromium controller (10X Genomics, CA) in conjunction with the single-cell 3 v2 kit. Briefly, the cell suspensions were diluted in nuclease-free water according to manufacturer instructions to achieve a targeted cell count of 5000. cDNA synthesis, barcoding and library preparation were then carried out according to the manufacturer's instructions. The libraries were sequenced on an Illumina Novaseq 6000 (Illumina, San Diego) with a read length of 26 bp for read 1 (cell barcode and unique molecule identifier (UMI)), 8bp i7 index read (sample barcode) and 98 bp for read 2 (actual RNA read).

Submitted by: Texas A&M University

Study: Single-cell RNA sequencing of lymphoblastoid cell lines (LCL) from two human populations.

PRJNA508890 • SRP172838 • All experiments • All runs

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Lymphoblastoid cell lines (LCLs) are the preferred choice of storage for patients' genetic material. Through the analysis of RNAs from LCLs, several mutations related with various diseases have identified. LCLs encompasses a wide range of metabolic pathways that are specific to individuals where the cells originated, making LCLs suitable for molecular and functional studies. Large-scale sequencing efforts have documented extensive genetic variation within the human populations. However, with the development of new methods to sequence the RNA at a single-cell level, our understanding of the origins, global distribution, and functional consequences of this variation now more far from complete than before. To better understand the spectrum of gene expression variation, we have sequenced two LCL samples (GM18502 and GM12878) derived from female donors of two human populations (YRI and CEU).

Sample: Single-Cell RNA-Seq GM12878

SAMN10532544 • SRS4238857 • All experiments • All runs

Organism: Homo sapiens

Library:

Name: GM12878

Instrument: Illumina NovaSeq 6000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Runs: 1 run, 474.4M spots, 142.3G bases, 50.8Gb

Run	# of Spots	# of Bases	Size	Published
SRR8427168	474,436,605	142.3G	50.8Gb	2019-01-10

ID:: 7071091

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