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Sample GSM1276582 Query DataSets for GSM1276582
Status Public on Nov 28, 2013
Title OKF4_control_rep2
Sample type RNA
Source name Oral keratinocyte
Organism Homo sapiens
Characteristics cell type: Oral keratinocyte
native mir196a expression: low
treatment: control
Growth protocol All cells were grown in KGM/Greens medium, as per standard protocols, to 60% confluence before trypsinisation
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cell pellets using RNEasy minikit (Qiagen), before quantificaiton and QC on an Agilent Bioanalyser
Label Cy3
Label protocol sample RNA together with the internal control transcripts were labelled with Cyanine 3-CTP (Cy3) dye during an amplification reaction using the Agilent Low Input Quick Amp Kit. The generated fluorescent cRNA (complimentary RNA) products were then purified using Qiagen’s RNeasy Mini Kit. Next, the yield of the linearly amplified cRNA and the Cy3 specific activity were quantified using the Microarray Measurement function of the NanoDrop spectrophotometer. To reduce its structure complexity, 600 ng cRNA of each sample were fragmented into approximately 50-200 bases long. The fragmentation step took place at 60 ºC for 30-min using a Fragmentation Mix for 8-pack microarray format.
Hybridization protocol 25µl of labelled and fragmented cRNA was hybridised onto Aglient Sureprint G3 60K arrays (8 per slide). The slides were placed in a hybridization rotator set to rotate at 10 rpm inside a 65 °C hybridization oven. After 17 hours, hybridized slides were disassembled and washed.
Scan protocol The arrays were scanned at 3 μm resolution using Agilent C Microarray Scanner pre-set with the default settings for a 8x60K G3 Microarray Format.
Description Gene expression in oral keratinocytes
Data processing Agilent Feature Extraction Software (version 10.5) was used to process the generated image files and create exportable data files containing all the parameters, computed statistical analysis, and feature results. The raw data (.txt) file was loaded into Qlucore Omics Explorer software, before normalisation by the 75th percentile shift method as implemented in the program
Submission date Nov 27, 2013
Last update date Nov 28, 2013
Contact name Keith David Hunter
Organization name University of Sheffield
Department School of Clinical Dentistry
Lab Oral Pathology
Street address Claremont Crescent
City Sheffield
State/province South Yorkshire
ZIP/Postal code S26 7YJ
Country United Kingdom
Platform ID GPL17077
Series (1)
GSE52810 The effect of miR196a of overall gene expression in oral keratinocytes

Data table header descriptions
VALUE Log2 75th percentile normalised Qlucore Omics output

Data table
A_19_P00315452 3.0105
A_19_P00315459 -0.5381
A_19_P00315482 0.56083
A_19_P00315492 -0.38675
A_19_P00315493 2.0214
A_19_P00315502 1.2584
A_19_P00315506 5.6666
A_19_P00315518 -0.23022
A_19_P00315519 -0.30865
A_19_P00315524 -0.27606
A_19_P00315528 1.8829
A_19_P00315529 1.7919
A_19_P00315538 1.507
A_19_P00315541 1.7144
A_19_P00315543 -0.20376
A_19_P00315550 -0.076368
A_19_P00315551 0.3599
A_19_P00315554 0.54884
A_19_P00315581 1.3926
A_19_P00315583 -1.086

Total number of rows: 50599

Table truncated, full table size 1089 Kbytes.

Supplementary file Size Download File type/resource
GSM1276582_US83603551_253949410762_S01_GE1_107_Sep09_2_2.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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