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Sample GSM2149825 Query DataSets for GSM2149825
Status Public on May 30, 2018
Title Untreated, rep3
Sample type RNA
 
Source name Bone marrow derived macrophage no treatment replicate 3
Organism Mus musculus
Characteristics background strain: C57BL/6
gender: female
tissue: bone marrow
cell type: macrophages
strain: C57BL6
Treatment protocol BMDMs were left untreated or stimulated with each ligand for 24 hours prior to wahing with phosphate buffered saline and the addition of fresh medium. Cells were then stimulted/re-stimulated with the appropriate TLR ligand for 4 hours prior to RNA extraction. Untreated cells were left untreated.
Growth protocol Bone marrow derived macrophages were isolated from female 6 - 8 week C57BL/6 mice and differentiated for 7 days in L929 conditioned growth medium
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Rneasy mini kit in combination with Qiashredders and a DNase step according to the manufacturers instructions (Qiagen).
Label Cy3
Label protocol Two hundred nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to fluorescent dye Cy3 using the Low Input Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.
 
Hybridization protocol Cy3-labeled cRNA (600 ng) from each sample was hybridized to an Agilent Mouse 8x60k Microarray. The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 10.7 (Agilent Technologies).
Scan protocol Cy3-labeled cRNA (600 ng) from each sample was hybridized to an Agilent Mouse 8x60k Microarray. The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 10.7 (Agilent Technologies).
Description UT_3
Gene expression after toll-like receptor ligand stimulation of macrophages
Data processing Data were pre-processed using limma R/Bioconductor package including RMA background correction, quantile normalisation and log2 transformation. Control probes were removed after normalisation. Detection threshold (log2) for Stemformatics graphing uses 95th percentile of negative control probe expression as per limma recommendation. Median expression is median (log2) of above-threshold expression of all non-control probes.
 
Submission date May 10, 2016
Last update date Feb 27, 2019
Contact name Othmar Korn
Organization name Australian Institute for Bioengineering and Nanotechnology
Street address University of Queensland
City St. Lucia
State/province Queensland
ZIP/Postal code 4067
Country Australia
 
Platform ID GPL10787
Series (1)
GSE81291 Comparison of gene expression in macrophages tolerised by different toll-like receptor ligands

Data table header descriptions
ID_REF
VALUE Log2 normalised signal intensity

Data table
ID_REF VALUE
A_30_P01017425 5.636699711
A_30_P01017426 4.865054846
A_30_P01017427 2.582371475
A_30_P01017428 5.165192123
A_30_P01017429 1.669029947
A_30_P01017430 4.182639944
A_30_P01017431 2.399602887
A_30_P01017432 3.873436048
A_30_P01017433 4.478365625
A_30_P01017434 5.66540851
A_30_P01017435 1.775487004
A_30_P01017436 8.052309515
A_30_P01017437 6.690869972
A_30_P01017438 1.775487004
A_30_P01017439 6.115874443
A_30_P01017440 3.518722594
A_30_P01017441 4.241921981
A_30_P01017442 6.603068826
A_30_P01017443 9.621561853
A_30_P01017444 5.982592698

Total number of rows: 55681

Table truncated, full table size 1407 Kbytes.




Supplementary file Size Download File type/resource
GSM2149825_UT_3.txt.gz 12.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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