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Sample GSM978897 Query DataSets for GSM978897
Status Public on Sep 12, 2012
Title RPE1_hTERT_WT_R1
Sample type RNA
Source name RPE-1 cell line, diploid cell line, replicate 1
Organism Homo sapiens
Characteristics cell line: RPE-1
multisomy/variation: WT
Treatment protocol no treatment
Growth protocol Both HCT116 and RPE-1 cell lines were cultured in DMEM (supplemented with 10% FBS) at 5% CO2, 37°C
Extracted molecule total RNA
Extraction protocol mRNA was purified using the Qiagen mRNeasy mini kit.
Label Cy3
Label protocol 500 ng (HCT116) or 100 ng (RPE-1) total RNA per sample were introduced into an RT-IVT reaction. Prior to RT-IVT, the total RNA samples were spiked with in-vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in-vitro transcription (HCT116: Quick-Amp Labeling Kit One-Color, Agilent Technologies; RPE-1: Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP according to the manufacturer´s instructions.
Hybridization protocol Following cRNA clean-up and quantification (NanoDrop ND-1000 Spectrophotometer, peqlab) 1.65 µg (HCT116) or 0.60 µg (RPE-1) of each Cyanin-3-labeled cRNA sample was fragmented and prepared for One-Color based hybridization (Gene Expression Hybridization Kit, Agilent). Each cRNA sample was hybridized at 65 °C for 17 hrs on separate Whole Human Genome Oligo Microarrays (4x44K format) (for HCT116) or SurePrint G3 Human Gene Expression Arrays (8x60K).
Scan protocol Fluorescent signal intensities were detected with Scan Control 8.1.3. Software (Agilent Technologies) (HCT116) or Scan Control A.8.4.1 Software (Agilent Technologie) (RPE-1) on the Agilent DNA Microarray Scanner.
Description Gene expression of RPE-1 cell lines
Data processing Signal intensities were extracted from the image using Feature Extraction 10.5.1 Software (Agilent Technologies) and the design file 014850_D_F_20090416.xml (HCT116) or Software and the design file 028004_D_F_20120130.xml (RPE-1). Data was background subtracted; log2 ratios calculated and normalized. Medians of replicates were calculated and a ratio of the aneuploid cell line (median) vs the corresponding WT cell line (median) was used for further analysis (indicated in the column header).
Submission date Jul 31, 2012
Last update date Sep 13, 2012
Contact name Gabriele Stoehr
Organization name MPI of Biochemistry
Department Proteomics ans Signaltransduction
Street address Am Klopferspitz 18
City Martinsried
ZIP/Postal code 82152
Country Germany
Platform ID GPL13607
Series (1)
GSE39768 Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

Data table header descriptions
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
1 4.653013e+004
2 2.771729e+000
3 4.661452e+000
4 2.396282e+002
5 1.344049e+003
6 1.712813e+001
7 3.884305e+003
8 9.516221e+002
9 7.609877e+000
10 5.127620e+001
11 2.928793e+000
12 1.178072e+003
13 9.193477e+002
14 4.359256e+002
15 1.369119e+004
16 2.971021e+000
17 2.088264e+002
18 2.980185e+000
19 6.435503e+000
20 8.009803e+002

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM978897_RS-254_01_RPE1_hTERT_1.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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