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Sample GSM634531 Query DataSets for GSM634531
Status Public on May 10, 2011
Title H23 Ctrl 24h 3
Sample type RNA
 
Source name Mouse forebrain primary cell cultue of astrocytes
Organism Mus musculus
Characteristics strain: C57 Bk6
age: 1.5 day
tissue: forebrain
cell type: primary cell culture astrocyte
treatment: Control
time: 24h
culture batch: 1
bead chip array sentrix code: 4421339033
Treatment protocol Monolayers of astrocytes were treated with Fasudil (diluted in astrocytic medium pre-warmed at 37ºC) and the volume was maintained at 0.5 ml per well. Vehicle-treated cultures were run in parallel to serve as controls.
Growth protocol Cells plated in 24-well plates (2.6 × 104 cells/cm2) and incubated in a humidified incubator at 36.5ºC with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted in one batch using the RNeasy Mini Kit and quality of the extracted RNA was determined using E-gene HAD-GT12 genetic analyser (John Morris Scientific, Melbourne, Australia).
Label biotin
Label protocol RNA was amplified using the Illumina® TotalPrep RNA Amplication Kit. Total RNA sample was reverse transcribed using T7 Oligo(dT) primer to generate first strand second strand cDNA. Biotinylated cRNA was generated from the double-stranded cDNA templates via in vitro transcription.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description replicate 3
Data processing Gene expression data was exported from Bead Studio using median shift normalization such that the lowest value is 1 and log2 transformed with the ‘Partek report plug-in’ (Partek® Inc., St. Louis, Missouri, U.S.A.) and analysed in Partek Genomics Suite. The resultant export file in project file format (.ppj) included log transformed signal intensity data and annotation. This file was then imported into Partek Genomics suite Version 6.3 (Partek® Inc., St. Louis, Missouri, U.S.A.). The normalised expression data was then exported from Partek, signal p values were not available for normalised expression values.
 
Submission date Dec 02, 2010
Last update date May 10, 2011
Contact name Victoria Mary Perreau
E-mail(s) vperreau@unimelb.edu.au
Phone +61 3 8344 1835
Organization name University of Melbourne
Department Center for Neuroscience
Street address Parkville
City Melbourne
State/province Victoria
ZIP/Postal code 3010
Country Australia
 
Platform ID GPL6885
Series (1)
GSE25829 TRANSCRIPTOMIC PROFILING OF ASTROCYTES TREATED WITH THE RHO KINASE INHIBITOR FASUDIL REVEALS CYTOSKELETAL AND PRO-SURVIVAL RESPONSESTRANSFORMATION INDUCED BY THE RHO KINASE INHIBITOR FASUDIL.

Data table header descriptions
ID_REF
VALUE Log transformed (base 2) normalized signal intensity

Data table
ID_REF VALUE
ILMN_3163582 5.99321
ILMN_3163581 6.01647
ILMN_3163577 6.13814
ILMN_3163567 5.46683
ILMN_3163554 5.50891
ILMN_3163543 6.27712
ILMN_3163529 6.60927
ILMN_3163527 5.48449
ILMN_3163526 5.73265
ILMN_3163514 5.33264
ILMN_3163504 7.10689
ILMN_3163490 5.57143
ILMN_3163486 6.50856
ILMN_3163481 6.88256
ILMN_3163428 6.92979
ILMN_3163424 5.99198
ILMN_3163419 6.05791
ILMN_3163403 8.3711
ILMN_3163399 5.26861
ILMN_3163363 5.46087

Total number of rows: 18116

Table truncated, full table size 369 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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