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Sample GSM1470332 Query DataSets for GSM1470332
Status Public on Mar 26, 2015
Title Ctrl_LPS rep1
Sample type RNA
 
Source name BMDM_Ctrl_LPS
Organism Mus musculus
Characteristics strain: Specific pathogen-free C57Bl/6
cell type: bone marrow-derived macrophage (BMDM)
stimulated: LPS for 6hrs
Treatment protocol BMDMs were stimulated with 10ng/ul ultrapure Ecoli lipopolysaccharide (LPS).
Growth protocol Specific pathogen-free C57Bl/6 mice were purchased from Harlan Sprague-Dawley (Horst, the Netherlands) and housed in a controlled environemt on 12h/12h light/dark cycles.
Extracted molecule total RNA
Extraction protocol Rneasy kit procedures including DNAse digestion.
Label biotin
Label protocol standard biotin Ambion labeling - Illumina
 
Hybridization protocol standard Illumina protocol
Scan protocol standard Illumina protocol
Description 7165861070_A
Data processing Estimated background was subtracted from the foreground for each bead. For replicate beads, outliers greater than 3 median absolute deviations from the median were removed and the average signal was calculated for the remaining intensities. For each probe a detection score was calculated by comparing its average signal with the summarized values for the negative control probes. Non-expressed probes were removed yielding 15978 expressed probes (detection p < 0.05). Expressed probe data were neqc normalized.
 
Submission date Aug 11, 2014
Last update date Mar 26, 2015
Contact name Brendon Scicluna
E-mail(s) brendon.scicluna@um.edu.mt
Organization name University of Malta
Street address Msida campus
City Msida
ZIP/Postal code MSD2020
Country Malta
 
Platform ID GPL6885
Series (1)
GSE60290 Genome-wide analysis of bone marrow-derived macrophage (BMDM) priming by Ifng and Ifnb.

Data table header descriptions
ID_REF
VALUE NEQC normalized
detection Pval

Data table
ID_REF VALUE detection Pval
ILMN_1212607 5.81067263 0.003931848
ILMN_1212619 5.070519822 0.187418087
ILMN_1212632 4.924627922 0.331585845
ILMN_1212636 10.59955963 0
ILMN_1212637 8.777775335 0
ILMN_1212648 7.950876472 0
ILMN_1212653 5.248505349 0.098296199
ILMN_1212672 5.062929442 0.193971166
ILMN_1212682 5.492271861 0.031454784
ILMN_1212685 4.781679601 0.596330275
ILMN_1212692 4.740087199 0.692005242
ILMN_1212693 4.740243563 0.692005242
ILMN_1212695 11.22400995 0
ILMN_1212703 6.021864088 0
ILMN_1212717 8.51059625 0
ILMN_1212720 7.282895133 0
ILMN_1212752 4.806287635 0.525557012
ILMN_1212759 8.187439416 0
ILMN_1212791 5.906023566 0
ILMN_1212794 6.147844006 0

Total number of rows: 15978

Table truncated, full table size 483 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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