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Sample GSM885549 Query DataSets for GSM885549
Status Public on Mar 06, 2012
Title Stretch 1 hour sample 7
Sample type RNA
Source name Stretch 1 hour
Organism Rattus norvegicus
Characteristics cell type: Primary alveolar epithelial cell
strain: Sprague Dawley
gender: male
weight: 200-300g
Treatment protocol Isolated type II cells from whole lung, grown for 5 days in MEM + 0.1x FBS until cells attain type I characteristics
Extracted molecule total RNA
Extraction protocol Quiagen miRNAeasy Kit per protocol; quality control with Agilent 2100 bioanalyzer
Label Hy5
Label protocol Adjust RNA and volume to 0.25ug to 1ug in 2ul of nuclease free water; add CIP buffer, enzyme, and spike-in RNA at 37C x 30min; quench 95C x 5min; snap cool on ice 2-15min; mix with Labeling buffer, enzyme, dye, and DMSO 16C x 1hr; quench 65C x 15min, cool to 4C; hybridization within 1 hour
Hybridization protocol Mix dyed samples with warmed hyb buffer; denature 95C x 3min; snap cool on ice 2-15min; centrifuge max 1min; apply sample to Agilent coverslip and slide, and assemble hyb apparatus; hyb 56C x 16hr rotation speed 4; wash 3x with buffers A, B, C 2min each, rinse with water, dry by centriguge 800rpm x 3min
Scan protocol Images acquired at 635 and 532 nm using GenePix 4000B, analyzed genePix pro
Description Each array was hybridized with each sample labeled with Hy5 against a Common Reference (labeled Hy3). Common Reference is an equal (same ng of RNA) mix of all sample groupings (Control, 1hr stretch, 6hr stretch) from each of the 12 individual samples pooled together.
Data processing The software was Partek Genomics Suite (version 6.4) where background subtracted intensities were extracted, any background intensity below 1 was changed to 1, and loess normalization was applied.
Submission date Mar 04, 2012
Last update date Mar 06, 2012
Contact name Nadir Yehya
Organization name University of Pennsylvania
Department Bioengineering
Street address 390 Towne Bldg, U Penn
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL7722
Series (1)
GSE36256 Differential expression of miRNA in stretched rat alveolar epithelial cells

Data table header descriptions
VALUE loess normalized intensity

Data table
-1 593
0 6.5
10138 1506
10306 661
10482 1
10618 58
10898 502
10899 8469
10901 13
10902 4
10903 6
10904 5501
10905 2770.5
10906 1321.5
10907 16841.5
10914 4854.5
10919 332.5
10923 297
10925 28
10928 1756.5

Total number of rows: 1279

Table truncated, full table size 11 Kbytes.

Supplementary file Size Download File type/resource
GSM885549_miRNA1162H_Ref__532_750__vs_8302__635_780__100708.gpr.gz 482.1 Kb (ftp)(http) GPR
Processed data included within Sample table

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