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There have been two recent reports that investigated gene expression variations between individuals with European ancestry and individuals with African ancestry (Nigeria) using lymphoblastoid cell lines [31], [32].
Because gemcitabine is used to treat a variety of solid tumors including pancreatic cancer, in order to validate this association obtained using lymphoblastoid cell lines, we selected two pancreatic tumor cell lines to perform siRNA knock down of three selected genes (MGMT, VAV3 and GPM6A) with expression levels that were associated with either or both of the rs3797418 and rs6082527 SNPs.
In agreement with previous studies using lymphoblastoid cell lines (18), our methylation analysis confirmed that GSDMB is highly methylated in primary blood leukocytes (Fig. 5).
Analysis of chimeric transcript expression using lymphoblastoid cell lines derived from t(1 11) translocation carriers demonstrated that such transcripts are indeed produced (Fig. 2A).
We performed a whole genome expression profiling using lymphoblastoid cell lines (LCLs) from four SCA28 patients and six unrelated healthy controls matched for sex and age.
The use of this cryptic splice site has previously been reported for the c.5074G>C/p.Asp1692His variant using lymphoblastoid cell lines (LCLs) or patient blood samples [ 25, 26].
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The standard curve, performed in duplicate, ranged from 100 ng to 0.01 ng per well for each qPCR plate using lymphoblastoid cell line DNA NA07019 (Coriell Cell Repositories, Camden, New Jersey).
Genotype and phased haplotype data were collected from the HapMap project ([31]; www.hapmap.org/), whilst expression data were collected from the NCBI Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/ ) for studies that have used lymphoblastoid cell lines, where the individuals used partially or completely overlapped with the individuals included in the HapMap project.
The third option is to use lymphoblastoid cell lines.
We used lymphoblastoid cell lines (LCLs) from healthy donors, selected for their extreme thiopurine susceptibility.
This is not surprising as the 1 K Genomes Project used lymphoblastoid cell lines through EBV transformation of B-lymphocytes [ 7].
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