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Sample GSM1208990 Query DataSets for GSM1208990
Status Public on Jan 29, 2014
Title OCIS 15
Sample type RNA
Source name Subject 5003_Posterior_Interior
Organism Homo sapiens
Characteristics subject id: 3
tissue: vaginal tissue
tissue location (a-p): Posterior
tissue location (p-d): Interior
tissue location (l-r): NA
Extracted molecule total RNA
Extraction protocol Samples were thawed on ice and mixed by repeat pipet disruption with 70% ethanol according to the procedure described in the technical protocol of the RNeasy Mini Kit (QIAGEN), which was used for subsequent purification according to the manufacturer instructions. This included an on-column DNase digestion with the RNase-free DNase kit (QIAGEN). The total RNAs were eluted once with 50 µL of RNase-free water.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 25ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 arrays (G4851B, Design ID 039494) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immediately put the slides with Agilent barcode facing up in a slide holder with an ozone-barrier slide cover on top of the array.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array(Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%). Raw data were extracted using the Agilent Feature Extraction software, version, protocol GE1_107_Sep09.
Description vaginal tissue sample
Data processing Microarray expression values were calculated using the gProcessed Signal, which was normalized via log2 transformation and quantile normalization in Partek® Genomics Suite (v.6.6, Partek Inc, St. Louis, MO). Control probe expression levels were removed during normalization. Expression changes due to batch effects between arrays have been removed.
Submission date Aug 14, 2013
Last update date Jan 29, 2014
Contact name Charles David Warden
Organization name City of Hope
Department Department of Molecular and Cellular Biology
Street address 1500 East Duarte Rd
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
Platform ID GPL17077
Series (1)
GSE49892 Global Expression of Molecular Transporters in the Human Vaginal Tract

Data table header descriptions
VALUE Normalized gene expression

Data table
A_23_P117082 11.0191
A_33_P3246448 3.52978
A_33_P3318220 2.77685
A_33_P3236322 2.30182
A_33_P3319925 3.93667
A_21_P0000509 7.61761
A_21_P0000744 6.92836
A_24_P215804 2.46429
A_23_P110167 12.137
A_33_P3211513 7.80134
A_23_P103349 2.15969
A_32_P61480 2.34659
A_33_P3788124 2.40612
A_33_P3414202 9.22391
A_33_P3316686 7.28855
A_33_P3300975 2.15718
A_33_P3263061 11.0258
A_33_P3261373 2.43972
A_24_P278460 6.90591
A_21_P0013109 2.37615

Total number of rows: 50599

Table truncated, full table size 1058 Kbytes.

Supplementary file Size Download File type/resource
GSM1208990_US92200304_253949410713_S01_GE1_107_Sep09_1_3.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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