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Sample GSM276722 Query DataSets for GSM276722
Status Public on Jun 01, 2008
Title ob/ob Saline treated-3
Sample type RNA
 
Source name ob/ob Saline treated-3 lung
Organism Mus musculus
Characteristics B6.V-Lepob/J mouse strain (Jackson Lab) gender- female, age- 1 month, n = 1, # of tissue = 1 tissue: Lung
Treatment protocol Saline treatment
Growth protocol no growth protocol
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's 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 10 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 ob/ob Saline treated Lung 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 ob/ob leptin-treated 1 month x 3 sets ob/ob saline-treated 1 month comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons).
 
Submission date Mar 21, 2008
Last update date Mar 24, 2008
Contact name vikas misra
E-mail(s) vmisra@jhsph.edu
Organization name Johns Hopkins University School of public health
Department Environmental health sciences
Lab Clarke G Tankersley
Street address 615 N. Wolfe street, E6609
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL339
Series (1)
GSE10915 Comparative analysis of gene expression in ob/ob leptin-treated and ob/ob saline-treated lungs.

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 627.7 P 0.000244
1415671_at 1715.1 P 0.000732
1415672_at 2355 P 0.000244
1415673_at 140.1 P 0.018555
1415674_a_at 679.7 P 0.000244
1415675_at 700.8 P 0.000732
1415676_a_at 1959.4 P 0.000244
1415677_at 411 P 0.000732
1415678_at 1419.4 P 0.000244
1415679_at 2790.5 P 0.000244
1415680_at 855.2 P 0.000732
1415681_at 662.2 P 0.000244
1415682_at 419.8 P 0.001953
1415683_at 1382.9 P 0.000244
1415684_at 307.4 P 0.000732
1415685_at 347.2 P 0.000244
1415686_at 1270.7 P 0.000244
1415687_a_at 4937.7 P 0.000244
1415688_at 1804.7 P 0.000244
1415689_s_at 584.8 P 0.001221

Total number of rows: 22690

Table truncated, full table size 621 Kbytes.




Supplementary file Size Download File type/resource
GSM276722.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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