|
| Status |
Public on May 25, 2011 |
| Title |
Malignant cervical carcinoma cell line; manipulated_MS751.pcDNA3.1.zeo.Drosha #1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Cluster 1: Drosha under-expressing cell line: construct to over-express Drosha in MS751 cell line; levels only reached 1.996x reference; miRNA profiles still clustered with Drosha under-expressing samples; replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: malignant cervical carcinoma cell line MS751
protocol: pcDNA3.1 zeo Drosha construct
cluster: Cluster 1
drosha expression: under-expression
|
| Treatment protocol |
Nil; pre-treatment
|
| Growth protocol |
Cell lines cultured under standard tissue culture conditions - incubated at 37C and in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Total RNA from each sample and the reference (the latter pooled First Choice Human RNA Survey Panel, Ambion, Austin, TX, USA) were labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labeling kit (Exiqon, Vedbaek, Denmark).
|
| |
|
| Channel 2 |
| Source name |
First Choice Human RNA Survey Panel, Ambion, Austin, TX
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Pooled human RNA from 20 anatomical sites
|
| Treatment protocol |
Nil; pre-treatment
|
| Growth protocol |
Cell lines cultured under standard tissue culture conditions - incubated at 37C and in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Total RNA from each sample and the reference (the latter pooled First Choice Human RNA Survey Panel, Ambion, Austin, TX, USA) were labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labeling kit (Exiqon, Vedbaek, Denmark).
|
| |
|
| |
| Hybridization protocol |
Test and reference RNA samples were mixed pair-wise and hybridized to the miRCURY LNA array platform version 8.0 (Exiqon, Vedbaek, Denmark), according to the manufacturer's instructions.
|
| Scan protocol |
As described in Muralidhar et al 2007, PMID 17471471
|
| Description |
MS751 pcDNA3.1 zeo Drosha #1
Biological replicate 7 of 8
|
| Data processing |
The resultant raw .txt files were processed using the Bioconductor package limma in the statistical software environment R. For most experimental conditions, microRNA profiling was performed on two experimental replicates, which were mean summarized. Mean foreground signal intensities were corrected for background noise using exponential-normal convolution model, while inter-array normalization was performed using variance stabilization algorithm vsn2. Drosha over-expression was defined as levels ≥2.0 fold greater than in normal cervical keratinocytes (as described in Muralidhar et al 2007, PMID 17471471). We used limma to fit a linear model with empirical Bayes moderated t-statistics, adjusting p-values for false discovery using the Benjamini-Hochberg method and applying a significance threshold of alpha=0.01.
|
| |
|
| Submission date |
Dec 20, 2010 |
| Last update date |
May 25, 2011 |
| Contact name |
Matthew Jonathan Murray |
| E-mail(s) |
mjm16@cam.ac.uk
|
| Phone |
07976413769
|
| Organization name |
MRC Cancer Cell Unit
|
| Department |
MRC/Hutchison Research Centre
|
| Lab |
2.5
|
| Street address |
Box 197, Hills Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0XZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11338 |
| Series (2) |
| GSE26175 |
Functional evidence that Drosha over-expression in cervical squamous cell carcinoma affects cell phenotype and microRNA profiles [miRNA] |
| GSE26177 |
Functional evidence that Drosha over-expression in cervical squamous cell carcinoma affects cell phenotype and microRNA profiles |
|
