RNA-Seq gene expression profiling of HepG2 cells: The influence of experimental factors and comparison with liver tissue

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Tyakht, Alexander V ^a   Ilina, Elena N ^a   Alexeev, Dmitry G ^a,b   Ischenko, Dmitry S ^a,b   Gorbachev, Alexey Y ^a   Semashko, Tatiana A ^a,c   Larin, Andrei K ^a,b   Selezneva, Oksana V ^a   Kostryukova, Elena S ^a,b,c   Karalkin, Pavel A ^d   Vakhrushev, Igor V ^d   Kurbatov, Leonid K ^d   Archakov, Alexander I ^d   Govorun, Vadim M ^a,b,e  

^a FEDERAL RESEARCH AND CLINICAL CENTER OF PHYSICAL CHEMICAL MEDICINE OF FEDERAL MEDICAL BIOLOGICAL AGENCY   (Russian Federation)

^b MOSCOW INSTITUTE OF PHYSICS AND TECHNOLOGY   (Russian Federation)

^c KAZAN FEDERAL UNIVERSITY   (Russian Federation)

^d INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

^e SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

Author keywords

Differential gene expression; Experimental factors; Helicos; HepG2; Liver; RNA Seq; SOLiD; Transcriptome

Indexed keywords

CARBOXYLIC ACID; TRANSCRIPTOME; MESSENGER RNA;

ARTICLE; CANCER PROGNOSIS; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATIONAL STUDY; DOWN REGULATION; DROPLET DIGITAL POLYMERASE CHAIN REACTION; EXPERIMENTAL DESIGN; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE OVEREXPRESSION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HEPG2 CELL LINE; HUMAN; HUMAN CELL; LIVER; LIVER CANCER; MITOSIS; POLYMERASE CHAIN REACTION; RNA SEQUENCE; TRANSCRIPTOMICS; UPREGULATION; CLUSTER ANALYSIS; GENETICS; HEP-G2 CELL LINE; LIVER TUMOR; METABOLISM; SEQUENCE ANALYSIS;

CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; HEP G2 CELLS; HUMANS; LIVER; LIVER NEOPLASMS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84925685106     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-1108     Document Type: Article

References (16)

1. Schwartz RE, Fleming HE, Khetani SR, Bhatia SN: Pluripotent stem cell-derived hepatocyte-like cells. Biotechnol Adv 2014, 32:504-513. 10.1016/j.biotechadv.2014.01.003.
2. Knasmüller S, Mersch-Sundermann V, Kevekordes S, Darroudi F, Huber WW, Hoelzl C, Bichler J, Majer BJ: Use of human-derived liver cell lines for the detection of environmental and dietary genotoxicants; current state of knowledge. Toxicology 2004, 198:315-328. 10.1016/j.tox.2004.02.008.
3. Mane SP, Evans C, Cooper KL, Crasta OR, Folkerts O, Hutchison SK, Harkins TT, Thierry-Mieg D, Thierry-Mieg J, Jensen RV: Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing. BMC Genomics 2009, 10:264. 10.1186/1471-2164-10-264.
4. Xiong Y, Chen X, Chen Z, Wang X, Shi S, Wang X, Zhang J, He X: RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet 2010, 42:1043-1047. 10.1038/ng.711.
5. Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, Kitano TK, Hodel MR, Petersen JF, Wyatt PW, Steenblock ER, Shah PH, Bousse LJ, Troup CB, Mellen JC, Wittmann DK, Erndt NG, Cauley TH, Koehler RT, So AP, Dube S, Rose KA, Montesclaros L, Wang S, Stumbo DP, Hodges SP, et al.: High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem 2011, 83:8604-8610. 10.1021/ac202028g.
6. Zgoda VG, Kopylov AT, Tikhonova OV, Moisa AA, Pyndyk NV, Farafonova TE, Novikova SE, Lisitsa AV, Ponomarenko EA, Poverennaya EV, Radko SP, Khmeleva SA, Kurbatov LK, Filimonov AD, Bogolyubova NA, Ilgisonis EV, Chernobrovkin AL, Ivanov AS, Medvedev AE, Mezentsev YV, Moshkovskii SA, Naryzhny SN, Ilina EN, Kostrjukova ES, Alexeev DG, Tyakht AV, Govorun VM, Archakov AI: Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells. J Proteome Res 2013, 12:123-134. 10.1021/pr300821n.
7. Ponomarenko EA, Kopylov AT, Lisitsa AV, Radko SP, Kiseleva YY, Kurbatov LK, Ptitsyn KG, Tikhonova OV, Moisa AA, Novikova SE, Poverennaya EV, Ilgisonis EV, Filimonov AD, Bogolubova NA, Averchuk VV, Karalkin PA, Vakhrushev IV, Yarygin KN, Moshkovskii SA, Zgoda VG, Sokolov AS, Mazur AM, Prokhortchouck EB, Skryabin KG, Ilina EN, Kostrjukova ES, Alexeev DG, Tyakht AV, Gorbachev AY, Govorun VM, et al.: Chromosome 18 transcriptoproteome of liver tissue and HepG2 Cells and targeted proteome mapping in depleted plasma: Update 2013. J Proteome Res 2014, 13:183-190. 10.1021/pr400883x.
8. Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M: An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74. 10.1038/nature11247.
9. Van Delft J, Gaj S, Lienhard M, Albrecht MW, Kirpiy A, Brauers K, Claessen S, Lizarraga D, Lehrach H, Herwig R, Kleinjans J: RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene. Toxicol Sci 2012, 130:427-439. 10.1093/toxsci/kfs250.
10. Lee L, Wang K, Li G, Xie Z, Wang Y, Xu J, Sun S, Pocalyko D, Bhak J, Kim C, Lee K-H, Jang Y, Yeom Y, Yoo H-S, Hwang S: Liverome: a curated database of liver cancer-related gene signatures with self-contained context information. BMC Genomics 2011,12(Suppl 3):S3. 10.1186/1471-2164-12-S3-S3.
11. Ross AC, Zolfaghari R: Regulation of hepatic retinol metabolism: perspectives from studies on vitamin A status. J Nutr 2004, 134:269S-275S.
12. Oshlack A, Wakefield MJ: Transcript length bias in RNA-seq data confounds systems biology. Biol Direct 2009, 4:14. 10.1186/1745-6150-4-14.
13. Costantini S, Di Bernardo G, Cammarota M, Castello G, Colonna G: Gene expression signature of human HepG2 cell line. Gene 2013, 518:335-345. 10.1016/j.gene.2012.12.106.
14. R Development Core Team: R: a language and environment for statistical computing. R foundation for statistical computing; 2010. http://www.r-project.org
15. Robinson MD, McCarthy DJ, Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140. 10.1093/bioinformatics/btp616.
16. Zhang B, Kirov S, Snoddy J: WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res 2005,33(Web Server issue):W741-W748.