The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines

PLoS ONE

Volumn 9, Issue 9, 2014, Pages

  Çalişkan, Minal ^a   Pritchard, Jonathan K ^b   Ober, Carole ^a   Gilad, Yoav ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ADULT; ARTICLE; B LYMPHOCYTE; CD20+ B LYMPHOCYTE; CELL CULTURE; CELL ISOLATION; COEFFICIENT OF VARIATION; CONTROLLED STUDY; COPY NUMBER VARIATION; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; EPSTEIN BARR VIRUS; FEMALE; FREEZE THAWING; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; HUMAN; HUMAN CELL; LYMPHOBLASTOID CELL LINE; MALE; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE TRAIT LOCUS; ADVERSE EFFECTS; CRYOPRESERVATION; FREEZING; GENETIC TRANSFORMATION; GENETICS; METABOLISM; MICROARRAY ANALYSIS; MIDDLE AGED; PHENOTYPE; TEMPERATURE; TRANSFORMED CELL LINE; YOUNG ADULT;

ADULT; B-LYMPHOCYTES; CELL LINE, TRANSFORMED; CRYOPRESERVATION; FREEZING; GENE EXPRESSION; GENE EXPRESSION PROFILING; HERPESVIRUS 4, HUMAN; HUMANS; MICROARRAY ANALYSIS; MIDDLE AGED; PHENOTYPE; TEMPERATURE; TRANSFORMATION, GENETIC; YOUNG ADULT;

EID: 84907000985     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0107166     Document Type: Article

References (33)

1. International HapMap C, Frazer KA, Ballinger DG, Cox DR, Hinds DA, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
2. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.
3. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, et al. (2007) Population genomics of human gene expression. Nat Genet 39: 1217-1224.
4. Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, et al. (2011) DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol 12: R10.
5. Akey JM, Biswas S, Leek JT, Storey JD (2007) On the design and analysis of gene expression studies in human populations. Nat Genet 39: 807-808; author reply 808-809.
6. Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, et al. (2008) High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 4: e1000214.
7. Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, et al. (2009) Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325: 1246-1250.
8. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
9. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
10. Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, et al. (2012) Dissecting the regulatory architecture of gene expression QTLs. Genome Biol 13: R7.
11. Mangravite LM, Engelhardt BE, Medina MW, Smith JD, Brown CD, et al. (2013) A statin-dependent QTL for GATM expression is associated with statininduced myopathy. Nature 502: 377-380.
12. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, et al. (2011) Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res 21: 447-455.
13. Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, et al. (2012) DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482: 390-394.
14. McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, et al. (2013) Identification of genetic variants that affect histone modifications in human cells. Science 342: 747-749.
15. Dolan ME, Newbold KG, Nagasubramanian R, Wu X, Ratain MJ, et al. (2004) Heritability and linkage analysis of sensitivity to cisplatin-induced cytotoxicity. Cancer Res 64: 4353-4356.
16. Peters EJ, Motsinger-Reif A, Havener TM, Everitt L, Hardison NE, et al. (2011) Pharmacogenomic characterization of US FDA-approved cytotoxic drugs. Pharmacogenomics 12: 1407-1415.
17. Hayashi A, Kasahara T, Kametani M, Toyota T, Yoshikawa T, et al. (2009) Aberrant endoplasmic reticulum stress response in lymphoblastoid cells from patients with bipolar disorder. Int J Neuropsychopharmacol 12: 33-43.
18. Jen KY, Cheung VG (2003) Transcriptional response of lymphoblastoid cells to ionizing radiation. Genome Res 13: 2092-2100.
19. Rose S, Frye RE, Slattery J, Wynne R, Tippett M, et al. (2014) Oxidative stress induces mitochondrial dysfunction in a subset of autism lymphoblastoid cell lines in a well-matched case control cohort. PLoS One 9: e85436.
20. Sarachana T, Zhou R, Chen G, Manji HK, Hu VW (2010) Investigation of post-transcriptional gene regulatory networks associated with autism spectrum disorders by microRNA expression profiling of lymphoblastoid cell lines. Genome Med 2: 23.
21. Caliskan M, Cusanovich DA, Ober C, Gilad Y (2011) The effects of EBV transformation on gene expression levels and methylation profiles. Hum Mol Genet 20: 1643-1652.
22. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
23. Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
24. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, et al. (2008) Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet 4: e1000287.
25. Gruhne B, Sompallae R, Masucci MG (2009) Three Epstein-Barr virus latency proteins independently promote genomic instability by inducing DNA damage, inhibiting DNA repair and inactivating cell cycle checkpoints. Oncogene 28: 3997-4008.
26. Jeon JP, Shim SM, Nam HY, Baik SY, Kim JW, et al. (2007) Copy number increase of 1p36.33 and mitochondrial genome amplification in Epstein-Barr virus-transformed lymphoblastoid cell lines. Cancer Genet Cytogenet 173: 122-130.
27. Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, et al. (2007) A survey of genetic human cortical gene expression. Nat Genet 39: 1494-1499.
28. Schadt EE, Molony C, Chudin E, Hao K, Yang X, et al. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6: e107.
29. Zeller T, Wild P, Szymczak S, Rotival M, Schillert A, et al. (2010) Genetics and beyond - the transcriptome of human monocytes and disease susceptibility. PLoS One 5: e10693.
30. Idaghdour Y, Storey JD, Jadallah SJ, Gibson G (2008) A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs. PLoS Genet 4: e1000052.
31. Grundberg E, Small KS, Hedman AK, Nica AC, Buil A, et al. (2012) Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet 44: 1084-1089.
32. Innocenti F, Cooper GM, Stanaway IB, Gamazon ER, Smith JD, et al. (2011) Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet 7: e1002078.
33. Nica AC, Parts L, Glass D, Nisbet J, Barrett A, et al. (2011) The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet 7: e1002003.