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Sample GSM227713 Query DataSets for GSM227713
Status Public on Sep 11, 2007
Title MNR 3-3 KO Treated 4
Sample type RNA
 
Source name Type II cells from Nrf2-/- mouse supplemented with GSH.
Organism Mus musculus
Characteristics ICR10 mouse strain (Nrf2-/-) gender- female, age- 2 months, n = 1, # of tissue = 1, tissue: Lung, Cell:Type II, Supplementation: GSH.
Treatment protocol no treatment
Growth protocol Type II cells were isolated by instilling and incubating lung with Dispase II for 45 munutes.lungs were teased and cells were incubated on IgG coated plates for an hour to remove lung macrophases. The non adherent cells were further incubated on petridishes for two hours for fibroblast adherence. The non adherent cells were cultured on fibronectin/collagen coated plates in the presense of keratinocyte growth factor for five days.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed followed by RNA clean up using Qiagen Rneasy kit according to the manufacturers' instructions.
Label ENZO BioArray HighYield RNA Transcript Labeling Kit
Label protocol cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).
 
Hybridization protocol Following fragmentation, 1 200 ul of hybridization cocktail containing 5 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)
Scan protocol Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.
Description Mouse Lung Type II cell gene expression
Data processing Data extraction was processed by Affy GeneChip® Operating Software v1.3 (Affymetrix). Global scaling was equal to 500. Normalization factor was equal to 1. Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix). 3 sets B6 18/26 months x 3 sets B6 2 months comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5
 
Submission date Sep 07, 2007
Last update date Aug 28, 2018
Contact name Narsa Reddy Machireddy
E-mail(s) nmachire@jhsph.edu
Phone 1-410-955-4711
Fax 1-410-955-0299
Organization name Bloomberg School of Public Health
Department Environmental Health Sciences
Lab Sekhar Reddy Lab
Street address 615, N Wolfe St
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL1261
Series (1)
GSE7810 Comparative analysis of gene expression WT and Nrf2-/- mice Type II cells
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE Affy GeneChip® Operating Software v1.3 Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1415670_at 2432.4 P 0.000244
1415671_at 5633 P 0.000244
1415672_at 5719.1 P 0.000732
1415673_at 852.9 P 0.000732
1415674_a_at 2537 P 0.000244
1415675_at 1146.2 P 0.000244
1415676_a_at 5650.6 P 0.000244
1415677_at 1228.1 P 0.000244
1415678_at 2459.8 P 0.000732
1415679_at 5216.9 P 0.000244
1415680_at 1392.9 P 0.000244
1415681_at 1701.5 P 0.000244
1415682_at 801.9 P 0.000244
1415683_at 4814.9 P 0.000244
1415684_at 1319.1 P 0.000244
1415685_at 1006 P 0.000244
1415686_at 3284.5 P 0.000244
1415687_a_at 18824.9 P 0.000244
1415688_at 2694.5 P 0.000244
1415689_s_at 862.1 P 0.000732

Total number of rows: 45101

Table truncated, full table size 1215 Kbytes.




Supplementary file Size Download File type/resource
GSM227713.CEL.gz 4.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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