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Sample GSM565797 Query DataSets for GSM565797
Status Public on Jul 16, 2010
Title 10-87LP3 vs 10-87HP3
Sample type RNA
 
Channel 1
Source name African Green Monkey Kidney Cells
Organism Chlorocebus aethiops
Characteristics cell type: non-tumorigenic
sample type: 10-87LP3
cell line: VERO
Biomaterial provider ATCC
Treatment protocol The cell lines has been passaged in culture under low density condition. Total RNA (including miRNAs) has been extracted at passage 148.
Growth protocol Cells from the World Health Organization (WHO) VERO cell bank 10–87 (ATCC 10–87 VERO cells) were serially passaged in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) (DMEM-10) from p134 to p250 by sub-culturing VERO cells before they reached confluence.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted and purified using the miRNeasy mini kit according to the manufacturer’s procedures (Qiagen Inc., Valencia, CA).
Label Cy3
Label protocol The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.
 
Channel 2
Source name African Green Monkey Kidney Cells
Organism Chlorocebus aethiops
Characteristics cell type: tumorigenic
sample type: 10-87HP3
cell line: VERO
Biomaterial provider Laborator of DNA Virus, FDA
Treatment protocol The cell lines has been passed in culture under low density condition and Total RNA (including miRNAs) was extracted at passage 250.
Growth protocol Cells from the World Health Organization (WHO) VERO cell bank 10–87 (ATCC 10–87 VERO cells) were serially passaged in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) (DMEM-10) from p134 to p250 by sub-culturing VERO cells before they reached confluence.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted and purified using the miRNeasy mini kit according to the manufacturer’s procedures (Qiagen Inc., Valencia, CA).
Label Cy5
Label protocol The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.
 
 
Hybridization protocol The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C. After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining. Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).
Scan protocol Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).
Description None
Data processing Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.
 
Submission date Jul 13, 2010
Last update date Jul 15, 2010
Contact name Andrew M Lewis
E-mail(s) andrew.lewis@fda.hhs
Phone 301-827-0650
Organization name Food and Drug Adminstration
Department Division of Viral products
Lab Labratory of DNA Virus
Street address 29 Lincoln Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL10649
Series (1)
GSE22920 Patterns of microRNA Expression in Non-Human Primate

Data table header descriptions
ID_REF
VALUE normalized log 2 ratio (10-87HP3/10-87LP3)
Signal A Mean Signal Intensity 10-87LP3
StDev A StDev 10-87LP3
Signal B Mean Signal Intensity 10-87HP3
StDev B StDev 10-87HP3

Data table
ID_REF VALUE Signal A StDev A Signal B StDev B
3151 0.45 6187.53 199.13 8427.49 188.38
619 0.35 6412.27 255.33 8148.49 320.56
1332 0.34 6371.63 249.13 8054.07 398.77
1415 0.96 583.01 65.83 1131.36 64.13
2293 0.83 638.02 70.86 1135.40 58.73
599 1.00 545.33 59.26 1088.65 108.31
3327 0.80 623.57 93.44 1086.91 60.11
2355 0.58 13405.20 243.88 20074.39 269.04
661 0.55 13531.44 212.00 19850.60 355.72
1477 0.55 13738.69 297.75 20051.52 339.79
3389 0.51 13361.25 295.97 19039.08 381.19
2386 -2.26 1434.61 91.54 300.44 29.90
3420 -2.15 1564.66 110.49 352.19 34.93
692 -2.06 1527.10 117.57 367.32 39.54
1508 -1.96 1359.63 99.69 349.87 41.23
816 2.28 441.44 54.35 2145.01 99.92
2510 2.24 431.13 42.85 2030.80 102.24
1632 2.25 459.22 31.67 2186.73 125.18
3544 2.14 472.47 75.48 2075.31 120.74
3730 0.56 16097.03 249.39 23759.14 383.21

Total number of rows: 3452

Table truncated, full table size 102 Kbytes.




Supplementary file Size Download File type/resource
GSM565797_01_PR10.0_071145_0910_395_530_Data_raw.txt.gz 128.8 Kb (ftp)(http) TXT
Processed data included within Sample table

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