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Sample GSM1250907 Query DataSets for GSM1250907
Status Public on Oct 29, 2013
Title Female WT, replicate C
Sample type RNA
 
Source name TGC-induced peritoneal macrophage
Organism Mus musculus
Characteristics gender: female
genotype: WT
cell type: macrophage
genetic background: C57BL/6 background, p38 floxed mice (Mapk14tm1.2Otsu) crossed with Lysm-Cre mice
Treatment protocol all samples were stimulated for 4 hrs with heat killed mycobacterium tuberculosis
Growth protocol macrophages were isolated on D4 post thioglycolate injection, adhered to plates overnight
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNEasy kit (Qiagen) according to manufacturer’s instructions. Microarray was performed on 3 biological replicates for each condition (e.g. female KO). To create each replicate, equal amounts of RNA from 2-3 different mice were pooled. An RNA input of 25ng was used to generate cDNA through the First Strand and Second Strand synthesis reactions of the Ovation® Pico WTA System V2 from NuGEN. The cDNA samples were then purified using an Agencourt® RNAClean® XP magnetic bead protocol. Following purification, samples were amplified using SPIA reagents from the Ovation® Pico WTA System V2 from NuGEN. A final cDNA purification is performed using an Agencourt® RNAClean® XP magnetic bead protocol.
Label biotin
Label protocol Approximately 4ug of cDNA generated using the Ovation® Pico WTA System V2 was fragmented and labeled using the Encore® Biotin Module from NuGEN. Efficiency of the biotin labeling reaction was verified using NeutrAvidin (10mg/mL) with a gel-shift assay.
 
Hybridization protocol Samples were injected into arrays and placed in the Affymetrix Genechip® Hybridization Oven 640 at 45° C and 60 RPM for 16-18 hours overnight.
Scan protocol Arrays were stained using the Affymetrix Genechip® Fluidics Station 450 and scanned with the Affymetrix Genechip® Scanner 3000.
Description Total RNA from Female WT (p38a-f/f) macrophages; pooled from 2-3 samples from individual mice, biological replicate 3
Data processing The signal intensity for each probe on each chip was calculated from scanned images using GeneChip Operating Software (Affymetrix), and signal intensities were analyzed using BioConductor (http://www.bioconductor.org). Probe intensities were background corrected, normalized, and summarized using the Robust Multichip Average method described by Speed and coworkers (Bolstad et al., 2003; Irizarry et al., 2003). An alternative normalization method based on housekeeping genes did not significantly change the results. Probe sets were considered differentially expressed when the signed fold change was ≥ 1.5, and the P-value was < 0.05.
MoGene-2_0-st.pgf
MoGene-2_0-st.mps
 
Submission date Oct 25, 2013
Last update date Nov 01, 2013
Contact name Dimitry Krementsov
E-mail(s) dkrement@uvm.edu
Organization name University of Vermont
Department BHSC
Street address 312C Rowell bldg, 106 Carrigan drive
City 89 Beaumont ave
State/province VT
ZIP/Postal code 05405
Country USA
 
Platform ID GPL16570
Series (1)
GSE51707 Sex-specific control of CNS autoimmunity by p38 MAPK signaling in myeloid cells

Data table header descriptions
ID_REF
VALUE log2 GC-RMA signal

Data table
ID_REF VALUE
17550444 11.23
17543785 11.13
17550478 11.38
17546287 4.10
17546316 4.20
17546797 4.19
17546834 4.28
17536979 6.15
17354757 6.31
17533498 8.31
17550472 7.57
17247500 5.57
17488799 8.13
17436907 6.10
17208191 6.62
17281885 5.28
17208509 6.27
17495262 8.25
17454973 6.96
17410204 7.04

Total number of rows: 41345

Table truncated, full table size 567 Kbytes.




Supplementary file Size Download File type/resource
GSM1250907_FWT-C-Teuscher-11-28-2012-PicoOvationV2_MoGene-2_0-st_.CEL.gz 8.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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