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Series GSE65314

Query DataSets for GSE65314

Status

Public on Jan 27, 2015

Title

Experimental gene expression analysis of 12 cancer cell lines

Organism

Homo sapiens

Experiment type

Expression profiling by array
Third-party reanalysis

Summary

The accurate choice of anti-cancer drugs is important problem of modern medicine. We developed a new method for the selection of targeted drugs based on detection of specific intracellular signaling and metabolic pathways in the bioinformatic system termed OncoFinder before the treatment.
We obtained transcriptomic data 12 human cancer cell lines (NT2/D1, Tera-1, NGP, HepG2, BT474, Skov-3, T3M4, HeLa, A549, MCF-7, Jurkat, BxPc1) before a treatment. In our research for gene expression quantile normalization of the experimental data of all 12 cell lines together, we used separately eleven gene expression datasets corresponding to different normal human tissues profiled on Illumina HT-12v3-4 platform, 4-33 samples per dataset (from GEO). Normalization datasets used for the processing of the experimental transcriptomic data: GSE17822 (GSM444688, GSM444689, GSM444690, GSM444691, GSM444692, GSM444693), GSE26852 (GSM661123, GSM661124, GSM661125, GSM661126, GSM661127, GSM661128, GSM661130), GSE32124 (GSM796359, GSM796360, GSM796361, GSM796362, GSM796363, GSM796364, GSM796365, GSM796366, GSM796367, GSM796368, GSM796369, GSM796370, GSM796371, GSM796372, GSM796373, GSM796374, GSM796375, GSM796376, GSM796377, GSM796378, GSM796379, GSM796380, GSM796381, GSM796382, GSM796383, GSM796384, GSM796385, GSM796386, GSM796387, GSM796388, GSM796389, GSM796390, GSM796391), GSE34074 (GSM841415, GSM841419, GSM841423, GSM841427, GSM841431, GSM841435), GSE37013 (GSM908514, GSM908515, GSM908516, GSM908517, GSM908518, GSM908519, GSM908520), GSE40645 (GSM998797, GSM998798, GSM998799, GSM998800, GSM998801, GSM998802, GSM998803, GSM998804, GSM998805, GSM998806, GSM998807, GSM998808, GSM998809, GSM998810), GSE42656 (GSM1047460, GSM1047462, GSM1047463, GSM1047467), GSE52130 (GSM1260102, GSM1260103, GSM1260104, GSM1260105, GSM1260106, GSM1260107, GSM1260108), GSE54563 (GSM1318920, GSM1318921, GSM1318922, GSM1318923, GSM1318924, GSM1318925, GSM1318926, GSM1318927, GSM1318928, GSM1318929, GSM1318930, GSM1318931, GSM1318932, GSM1318933, GSM1318934, GSM1318935, GSM1318936, GSM1318937, GSM1318938, GSM1318939, GSM1318940, GSM1318941, GSM1318945, GSM1318946, GSM1318947), GSE57218 (GSM1380887, GSM1380888, GSM1380956, GSM1380957, GSM1380958, GSM1380959), GSE60709 (GSM1486145, GSM1486146, GSM1486160, GSM1486161, GSM1486162, GSM1486163, GSM1486164, GSM1486165, GSM1486166, GSM1486167, GSM1486168, GSM1486169, GSM1486170, GSM1486171, GSM1486172, GSM1486173). Normalization of the 12 new cell line data was performed independently 11 times together with the data from the GSM ID numbers listed above. For GSM1486145, data for replicate samples 34 and 35 were used. For sample GSM1486146, data for replicate sample 36 was used.

Overall design

Total RNA obtained from NT2/D1, Tera-1, NGP, HepG2, BT474, Skov-3, T3M4, HeLa, A549, MCF-7, Jurkat, BxPc1 cell lines.

Contributor(s)

Venkova L, Buzdin A

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Submission date

Jan 26, 2015

Last update date

Aug 13, 2018

Contact name

Larisa Venkova

E-mail(s)

venkovals@gmail.com

Organization name

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

Lab

Laboratory for Genomic Analysis of Cell Siganaling

Street address

Miklukho-Maklaya, 16/10

City

Moscow

ZIP/Postal code

117997

Country

Russia

Platforms (1)

GPL10558

Illumina HumanHT-12 V4.0 expression beadchip

Samples (12)

More...

GSM1592329	NT2D1
GSM1592330	NGP
GSM1592331	HepG2

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BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE65314_GSE17822_normalization.txt.gz	1.6 Mb	(ftp)(http)	TXT
GSE65314_GSE26852_normalization.txt.gz	1.3 Mb	(ftp)(http)	TXT
GSE65314_GSE32124_normalization.txt.gz	3.9 Mb	(ftp)(http)	TXT
GSE65314_GSE34074_normalization.txt.gz	1.3 Mb	(ftp)(http)	TXT
GSE65314_GSE37013_normalization.txt.gz	1.7 Mb	(ftp)(http)	TXT
GSE65314_GSE40645_normalization.txt.gz	2.3 Mb	(ftp)(http)	TXT
GSE65314_GSE42656_normalization.txt.gz	1.4 Mb	(ftp)(http)	TXT
GSE65314_GSE52130_normalization.txt.gz	1.7 Mb	(ftp)(http)	TXT
GSE65314_GSE54563_normalization.txt.gz	2.6 Mb	(ftp)(http)	TXT
GSE65314_GSE57218_normalization.txt.gz	1.2 Mb	(ftp)(http)	TXT
GSE65314_GSE60709_normalization.txt.gz	2.6 Mb	(ftp)(http)	TXT
GSE65314_Non-normalized_data_12_cancer_cell_lines.txt.gz	2.3 Mb	(ftp)(http)	TXT
GSE65314_Non-normalized_data_12_cancer_cell_lines_with_annotation.txt.gz	15.9 Mb	(ftp)(http)	TXT
GSE65314_RAW.tar	26.2 Mb	(http)(custom)	TAR
Processed data are available on Series record