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| Status |
Public on Aug 23, 2010 |
| Title |
Pglyrp3_Untr_3 |
| Sample type |
RNA |
| |
|
| Source name |
Colon RNA, untreated
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c Pglyrp3-/-
tissue: colon
|
| Treatment protocol |
Mice (female, 8-9 weeks old) were either untreated or treated with oral solution of 5% dextran sulfate sodium (DSS) in drinking water for 48 hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the entire colon from each mouse using the TRIZOL method (InVitrogen), followed by digestion with RNase-free DNase (Qiagen) and purification on RNeasy spin columns using RNeasy Minikit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated sense strand DNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® Whole Ttranscript Sense Target Labeling Assay Manual, Afymetrix) at the Indiana University School of Medicine Center for Medical Genomics core facility.
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| |
|
| Hybridization protocol |
The hybridization was done at the Indiana University School of Medicine Center for Medical Genomics core facility using the protocols provided by Affymetrix GeneChip® Technical Manual. Following fragmentation labeled DNA was hybridized for 17 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.
|
| Scan protocol |
The scanning was done at the Indiana University School of Medicine Center for Medical Genomics core facility using standard protocols provided by Affymetrix GeneChip® Technical Manual.
|
| Description |
n/a
|
| Data processing |
The hybridization intensity data were analyzed with Partek Genomics Suite using defaults for RMA, which includes quantile normalization, RMA background correction and Median Polish Probe set Summarization. Only genes reliably expressed (with expression intensity of log2>6) were used for analysis. Genes with average expression signal from all groups of log2<6 are not included in the Matrix templates. Log2 values were used for direct statistical comparisons of expression signals, whereas anti-log2 values were used to calculate fold increases in gene expression between untreated and DSS-treated mice. Four Matrix templates are provided. In each template induction of gene expression by DSS treatment in mice lacking one Pglyrp gene (Pglyrp1, Pglyrp2, Pglyrp3, or Pglyrp4) is compared to the induction of gene expression by DSS in WT mice. The fold induction of mRNA in the colon of WT mice treated with DSS to untreated WT mice (column S in each Matrix template) was calculated for each gene on the array as follows: (anti-log2 signal for WT DSS mRNA)/(average anti-log2 signal for untreated WT mRNA). The fold induction of mRNA in the colon of Pglyrp-/- mice treated with DSS to untreated Pglyrp-/- mice (column AL in each Matrix template) was calculated for each gene on the array as follows: (anti-log2 signal for Pglyrp-/- DSS mRNA)/(average anti-log2 signal for untreated Pglyrp-/- mRNA). The significance of differences between the fold induction of mRNA in WT versus Pglyrp-/- mice for each gene on the array was calculated by t-test (column AN in each Matrix template). The ratio of the fold induction of mRNA in the colon of Pglyrp-/- mice treated with DSS to WT mice treated with DSS (column AT in each Matrix template) was calculated for each gene on the array as follows: [(anti-log2 signal for Pglyrp DSS mRNA)/(average anti-log2 signal for untreated Pglyrp mRNA)] / [(anti-log2 signal for WT DSS mRNA)/(average anti-log2 signal for untreated WT mRNA)]. The genes in each Matrix template are arranged in descending order from the highest to the lowest ratio of gene induction in Pglyrp-/- mice versus WT mice (column AT in each Matrix template).
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| |
|
| Submission date |
Nov 03, 2009 |
| Last update date |
Aug 23, 2010 |
| Contact name |
Roman Dziarski |
| E-mail(s) |
[email protected]
|
| Phone |
219-980-6535
|
| Organization name |
Indiana University School of Medicine-Northwest
|
| Street address |
3400 Broadway
|
| City |
Gary |
| State/province |
IN |
| ZIP/Postal code |
46408 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE18859 |
Gene expression in the colon of DSS-treated Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice |
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