NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM152258 Query DataSets for GSM152258
Status Public on Aug 31, 2007
Title B6 2months-3
Sample type RNA
 
Source name B6 2m-3 Lung
Organism Mus musculus
Characteristics C57BL/6J mouse strain (Jackson Lab) gender- male, age- 2 months, n = 1, # of tissue = 1 tissue: Lung
Treatment protocol no 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 B6 Lung gene expression
Data processing Data extraction was processed by Affy GeneChipĀ« 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 Dec 21, 2006
Last update date Aug 28, 2018
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 GPL1261
Series (1)
GSE6591 Comparative analysis of gene expression in C57BL/6J and DBA/2J aging lungs.
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 990.6 P 0.000244
1415671_at 3374.7 P 0.000244
1415672_at 4345.1 P 0.000244
1415673_at 237.8 P 0.001953
1415674_a_at 1315.1 P 0.000244
1415675_at 966.8 P 0.000244
1415676_a_at 2894.9 P 0.000244
1415677_at 800.7 P 0.00415
1415678_at 2124.3 P 0.000244
1415679_at 4433.8 P 0.000244
1415680_at 1001.5 P 0.000732
1415681_at 1035.5 P 0.000244
1415682_at 745.8 P 0.000244
1415683_at 2014.5 P 0.000244
1415684_at 833.6 P 0.000244
1415685_at 718 P 0.000244
1415686_at 2257.3 P 0.000244
1415687_a_at 8635.6 P 0.000244
1415688_at 3006.5 P 0.000244
1415689_s_at 848.4 P 0.000732

Total number of rows: 45101

Table truncated, full table size 1223 Kbytes.




Supplementary file Size Download File type/resource
GSM152258.CEL.gz 4.1 Mb (ftp)(http) CEL
GSM152258.EXP.gz 338 b (ftp)(http) EXP

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap