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Sample GSM120398 Query DataSets for GSM120398
Status Public on Dec 02, 2006
Title AJ 2-10
Sample type RNA
 
Source name AJ 1 Caroitd body
Organism Mus musculus
Characteristics A/J mouse strain (Jackson Lab) gender- male, age- 28 days, n = 20, # of tissue = 40 tissue: carotid body
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 A/J carotid body 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 A/J x 3 sets DBA/2J comparison (1.5 fold cutoff, Mann-Whitney test < 0.05, 6 out of 9 comparisons)
 
Submission date Jul 14, 2006
Last update date Oct 16, 2006
Contact name Alexander Balbir
E-mail(s) abalbir@jhsph.edu
Fax 410-955-0299
Organization name Johns Hopkins Bloomberg School of Public Health
Department Environmental Health Sciences
Lab Division of Physiology
Street address 615 N. Wolfe St. Room E7610
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL1261
Series (1)
GSE5313 Comparative analysis of gene expression in A/J CB versus DBA/2J

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
1449236_at 155.1 A 0.067627
1447207_at 167.8 P 0.030273
1456458_at 157.3 A 0.466064
1443329_at 5.6 A 0.850342
1429722_at 1724.4 P 0.000244
1423815_at 273.6 P 0.018555
1450553_at 30.8 A 0.72583
1452582_at 1350.7 P 0.000244
1442760_x_at 817.6 P 0.000244
1441788_s_at 79.8 P 0.005859
1448345_at 1136.4 P 0.046143
1446216_at 66.5 A 0.303711
1442338_at 117.9 P 0.023926
1426702_at 64.2 A 0.219482
1428731_at 767 A 0.129639
1440309_at 258.1 A 0.129639
1417516_at 634.9 P 0.000244
1419645_at 1124.2 P 0.00293
1445283_at 3.9 A 0.99585
1426046_a_at 409.9 A 0.171387

Total number of rows: 45101

Table truncated, full table size 1222 Kbytes.




Supplementary data files not provided

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