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Sample GSM1025306 Query DataSets for GSM1025306
Status Public on Feb 06, 2013
Title macrophages_treated_with_LPS+PGE_1hr_rep_2
Sample type RNA
Source name primary bone marrow derived mouse macrophages, treated with LPS and PGE, harvested after 1 hour of treatment
Organism Mus musculus
Characteristics strain: C57Bl/6 wild type mouse
cell type: primary macrophages
tissue: bone marrow
Treatment protocol BMDMs were either left untreated or stimulated with 100 ng/ml LPS (#L6529; Sigma) or a combination of 100 ng/ml LPS and 10 microM prostaglandin E for 1 hour
Growth protocol To obtain primary bone marrow derived mouse macrophages (BMDMs), bone marrow cells were maintained on bacterial grade plates for 1 week in DMEM supplemented with 10% heat inactivated FBS (Biosera), 2 mM L-glutamine, 100 units/ml penicillin G, 100mg/ml streptomycin, 0.25 mg/ml amphotericin (Invitrogen) and 5 ng/ml mCSF (R&D systems). Adherent cells were then re-plated on tissue culture grade plates in fresh media and used 24 hours after re-plating. RAW264.7 cells were cultured in DMEM supplemented with 10% heat inactivated FBS, 2 mM L-glutamine, 100 units/ml penicillin G and 100mg/ml streptomycin.
Extracted molecule total RNA
Extraction protocol RNA extraction was carried out by homogenisation of BMDMs in Trizol followed by phenol chloroform extraction.
Label biotin
Label protocol 250 ng of total RNA was used from each sample. The total RNAs were processed with Ambion WT Expression kit (P/N 4411973) and Affymetrix Genechip® WT Terminal Labelling and Controls Kit (P/N 901524), according to manufactures protocols. RNA concentration was checked with Nanodrop ND-2000 and Agilent Bioanalyzer electrophoresis station was used for quality control.
Hybridization protocol Samples were hybridized to Affymetrix Mouse Gene 1.1 ST array plate using manufacturer's protocols for using the GeneTitan® Hybridization, Wash and Stain Kit for WT Array Plates (P/N 901622)
Scan protocol GeneTitan® Instrument was used to hybridize, wash, stain and scan the arrays. Affymetrix GeneChip® Command Console® (AGCC) 3.1 was used to control GeneTitan® hybridization process and in summarizing probe cell intensity data (.CEL file generation). The hybridization quality was checked with AGCC and Expression Console 1.1.
Data processing The data analysis was carried out using Affymetrix Power Tools (APT), R (version 2.13.1) – Bioconductor and Partek GS 6.5 (version 6.11.0321) software. For quality control and probesets annotations, the latest annotations files (Release 32, dated 23-06-2011) downloaded from Affymetrix were used. Using APT, The probe level expression data were summarised to transcript cluster level, filtered to include DABG (detected above background) and normalised using two different normalisation methods – RMA and Plier-GCBA (GC background-adjusted). The dataset quality was analysed from spike in probesets, principal component analysis, hierarchical clustering analysis and by generating various quality control plots such as mean raw signal intensity plots, mean absolute deviation (MAD) of the residuals plots and probe cell intensity plots. The processed dataset submitted here (matrix table) shows quality control passed, DABG (detected above background) filtered data summarised to transcript cluster level and normalised using RMA normalisation method using Affymetrix Power Tools.
Submission date Oct 25, 2012
Last update date Feb 06, 2013
Contact name Manikhandan A V Mudaliar
Organization name University of Glasgow
Department College of Medical, Veterinary and Life Sciences
Lab Institute of Infection, Immunity and Inflammation
Street address Room B528, Sir Graeme Davies Building, 120 University Place
City Glasgow
State/province Scotland
ZIP/Postal code G12 8TA
Country United Kingdom
Platform ID GPL11533
Series (1)
GSE41833 Expression profiles of primary bone marrow derived mouse macrophages – untreated and treated with LPS or LPS+PGE

Data table header descriptions
VALUE RMA normalised, log2 transformed and DABG (detected above background) filtered transcript cluster level signal

Data table
10338001 11.45808
10338002 4.79
10338003 9.72049
10338004 6.70562
10338006 2.42318
10338007 2.97165
10338009 6.55368
10338011 4.37377
10338013 1.82785
10338017 12.66387
10338018 5.01804
10338019 3.96014
10338025 6.48991
10338026 12.91643
10338027 5.44188
10338028 3.7285
10338029 9.31959
10338032 1.979
10338033 5.0877
10338034 3.13358

Total number of rows: 35309

Table truncated, full table size 586 Kbytes.

Supplementary file Size Download File type/resource
GSM1025306_1h_PGE_LPS2_B05.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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