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Sample GSM563517 Query DataSets for GSM563517
Status Public on Jul 01, 2011
Title 6604-anti-miR-191
Sample type RNA
 
Source name Hepatocellular carcinoma, Hep3B2.1-7
Organism Homo sapiens
Characteristics cell line: Hepatocellular carcinoma, Hep3B2.1-7
treatment: anti-miR-191
Treatment protocol Cells were transfected with Oligofectamine (Invitrogen, Cat# 12252011) according to manufacturer instructions
Growth protocol Cells were grown in MEM–Eagle (+Earl's BBS), w/NEAA and 10% FBS with additions of sodium bicarbonate and sodium pyruvate.
Extracted molecule total RNA
Extraction protocol EZ-RNA II kit from Biological Industries, Israel, was used for total RNA extraction from cell lines
Label Cy5
Label protocol Fifteen micrograms of total RNA was labeled by ligation of an RNAlinker p-rCrU-Cy-dye
 
Hybridization protocol Labeled RNA was mixed with 33 hybridization buffer (Ambion), heated to 95 C for 3 min, and incubated with the miRdicator array for 12–16 hr
Scan protocol Arrays were scanned using Agilent DNA Microarray Scanner Bundle (Agilent Technologies, Santa Clara, CA) at a resolution of 10 mm at 100% power. Array images were analyzed using SpotReader software (Niles Scientific, Portola Valley, CA).
Description 6604
Data processing Triplicate spots were combined to produce one signal for each probe by taking the logarithmic mean of reliable spots. All data were log-transformed (base 2) and the analysis was performed in log-space. A reference data vector for normalization R was calculated by taking the median expression level of a subset of all probes (all miRs in mirbase 10) across samples. For each sample data vector S, a 2nd degree polynomial F was found so as to provide the best fit between the sample data and the reference data, such that R≈F(S). For each probe in the sample (element Si in the vector S), the normalized value (in log-space) Mi was calculated from the initial value Si by transforming it with the polynomial function F, so that Mi=F(Si). P-values were calculated using a two-sided t-test on the log-transformed normalized fluorescence signal. The fold-difference (ratio of the median normalized fluorescence) was calculated for each microRNA.
 
Submission date Jul 07, 2010
Last update date Jul 01, 2011
Contact name Einat Sitbon
Organization name Rosetta Genomics
Street address 10 Plaut St
City Rehovot
ZIP/Postal code 76706
Country Israel
 
Platform ID GPL10651
Series (2)
GSE22793 miR expression after treatment with anti-miR-191 or control
GSE22910 hsa-miR-191, a potential target for Hepatocellular carcinoma therapy

Data table header descriptions
ID_REF
VALUE log2 normalized signal

Data table
ID_REF VALUE
hsa-let-7a-14714 10.90633608
hsa-let-7b-14712 9.844018619
hsa-let-7c-14713 11.2300793
hsa-let-7f-14715 5.993436617
hsa-miR-100-15240 10.16503731
hsa-miR-101-14841 5.64385619
hsa-miR-103-15129 15.38751675
hsa-miR-106a-15196 15.39356952
hsa-miR-106b-14862 11.89779579
hsa-miR-107-15130 15.32458696
hsa-miR-10a-14834 5.64385619
hsa-miR-122a-14682 5.690679498
hsa-miR-124a-14642 5.64385619
hsa-miR-125b-14765 11.53330965
hsa-miR-126*-15014 5.64385619
hsa-miR-128a-14786 6.871789127
hsa-miR-128b-14787 7.399327516
hsa-miR-130a-15021 5.64385619
hsa-miR-130b-15022 11.04086336
hsa-miR-132-14857 5.64385619

Total number of rows: 719

Table truncated, full table size 20 Kbytes.




Supplementary file Size Download File type/resource
GSM563517.srr.gz 226.4 Kb (ftp)(http) SRR
Processed data included within Sample table

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