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Sample GSM108080 Query DataSets for GSM108080
Status Public on May 12, 2006
Title Substantia Nigra Control Sample3 RMA, MAS 5, dChip
Sample type RNA
 
Source name Pooled Substantia Nigra C57BL/6 Saline injection
Organism Mus musculus
Characteristics Strain: C57BL/6
Gender: Male
Age: 10 Weeks
Tissue: Substantia Nigra(SN) dissected bilaterally from six like-treated mice.
Treatment protocol Mice received 4 injections of 0.9% sterile saline, of equal volume to treatment group. The first and second doses were separated by 16 hr. Mice were killed 24hr or 7d after injection. The SN was dissected bilaterally from six like-treated mice, pooled and RNA was prepared from Trizol homogenates per the manufacturer's protocol. (Invitrogen)
Extracted molecule total RNA
Extraction protocol Trizol
Label Biotinylated UTP & CTP
Label protocol Enzo IVT Protocol
 
Hybridization protocol Affymetrix Standard
Scan protocol Affymetrix Standard using U74A mask file
Description MAS 5.0, scaled to 500; Affymetrix Data Mining Tool 3.0; dChip was used to determine differentially expressed genes (MBEI); Statisticaly Analysis of Microarrays (SAM), as described in Miller et al. 2004.
Data processing Raw intensity data acquired from Affymetrix platform were RMA Normalized.
 
Submission date May 05, 2006
Last update date Sep 12, 2006
Contact name Howard J Federoff
Phone (585) 273-2190
URL http://www.urmc.rochester.edu/gebs/faculty/Howard_Federoff.htm
Organization name University of Rochester
Department Center for Aging and Developmental Biology
Lab Federoff
Street address 601 Elmwood Ave Box 645
City Rochester
State/province NY
ZIP/Postal code 14642
Country USA
 
Platform ID GPL32
Series (1)
GSE4788 Dysregulation of Gene Expression in the 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine-Lesioined Mouse Substantia Nigra

Data table header descriptions
ID_REF
VALUE RMA normalized intensity value
MAS5 MAS 5.0 normalized intensity value
dChip dChip normalized intensity value

Data table
ID_REF VALUE MAS5 dChip
100000_at 9.049057831 116.6 869.227
100001_at 9.25545544 52.4 1170.79
100002_at 12.65836948 3745.6 11430.4
100003_at 9.841370398 318 2850.54
100004_at 10.94997771 1457.6 2294.05
100005_at 11.98236316 2426 19372.7
100006_at 9.927161929 1149.8 11733
100007_at 12.98681749 4988.8 18168.1
100008_at 8.709123475 129.1 2326.2
100009_r_at 12.38682092 6735.5 10085.2
100010_at 11.27213914 184.8 6956.8
100011_at 10.49896386 1271.6 3839.49
100012_at 13.20740168 1409.2 18671.3
100013_at 10.48127899 130.5 5373.02
100014_at 10.02309685 440.1 4593.01
100015_at 10.53008463 460.7 20894.2
100016_at 9.591489714 420.7 20786.8
100017_at 10.31535881 921.3 2261.12
100018_at 11.98800638 525 17924.5
100019_at 11.70748529 1148.9 8306.41

Total number of rows: 12654

Table truncated, full table size 440 Kbytes.




Supplementary file Size Download File type/resource
GSM108080.CEL.gz 3.4 Mb (ftp)(http) CEL

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