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Sample GSM81022 Query DataSets for GSM81022
Status Public on Apr 29, 2006
Title E19_epithelial cells_control1
Sample type RNA
 
Source name E19 type II epithelial cells, 16h, control
Organism Rattus norvegicus
Characteristics Strain:CD
Gender:male and female
Age: Embryonic day 19
Tissue: Fetal lung from time-pregnant rats
Cells: Type II epithelial cells
Biomaterial provider Juan Sanchez-Esteban
Treatment protocol After isolation, E19 type II cells were cultured on silastic membranes coated with collagen 1. Next day monolayers were maintained on non-strained conditions for 16 h (control)
Growth protocol Cells were maintained in serum-free DMEM medium.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from E19 type II cells using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA) and purified further using the Rneasy Mini Kit (Invitrogen).
Label biotin
Label protocol conversion of double stranded cDNA into biotin-labeled cRNA was accomplished using the BioArray High Yield RNA Transcript Labeling kit (T7) (Enzo Diagnostics, Farmingdale, NY) according to the manufacturer’s instructions.
 
Hybridization protocol After hybridization cocktails preparation, the Affymetrix rat E230A GeneChip array was hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual.
Scan protocol GeneChips, bound to streptavidin-phycoerythrin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Agilent G2500A GeneArray Scanner (Agilent Technologies).
Description Total RNA was extracted from E19 type II cells using TRIzol reagent and the Rneasy Mini Kit. RNA was reverse-transcribed into cDNA with a T7-(dT)24 oligomer to prime the first-strand synthesis. DNA polymerase and DNA ligase were included in the synthesis of the second strand. After phase lock gel phenol/chloroform cDNA extraction and ethanol precipitation, double stranded cDNA was converted into cRNA. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Affymetrix GeneChip Expression Analysis Protocol. After hybridization cocktails preparation, the Affymetrix rat E230A GeneChip array was hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual. GeneChips, bound to streptavidin-phycoerythrin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Agilent G2500A GeneArray Scanner
Data processing Data were processed using Microarray Suite software, v. 5.0 (MAS 5.0) to yield expression values. These values were calculated from the difference in signal intensity following hybridization with "perfect match" (PM) and "mismatch" (MM) oligonucleotides in each probe
 
Submission date Oct 29, 2005
Last update date Nov 01, 2005
Contact name Juan Sanchez-Esteban
E-mail(s) jsanchezesteban@wihri.org
Phone 401-2741122 ext1383
Fax 401-4537571
Organization name Women & Infants Hospital/Brown Medical School
Department Pediatrics
Street address 101 Dudley Street
City Providence
State/province RI
ZIP/Postal code 02905
Country USA
 
Platform ID GPL341
Series (1)
GSE3541 DNA microarray reveals novel genes induced by mechanical forces in fetal lung type II epithelial cells

Data table header descriptions
ID_REF
VALUE signal, MAS5 transformation
ABS_CALL detection
DETECTION P-VALUE MicroArray Suite 5.0

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1398836_s_at 28617.1 P 0.000244
AFFX_Rat_beta-actin_3_at 27325.3 P 0.000044
1375170_at 27204.5 P 0.000244
1398835_at 27068.4 P 0.000244
AFFX_Rat_beta-actin_M_at 26301.8 P 0.000044
1371297_at 25061.9 P 0.000244
1389956_a_at 24322.5 P 0.000244
1371307_at 24275.7 P 0.000244
1371344_at 24004.9 P 0.000244
1387890_at 23906 P 0.000244
AFFX-r2-P1-cre-3_at 23678.7 P 0.000244
1371318_at 23464.6 P 0.000244
1367579_a_at 23369.9 P 0.000244
1370242_at 23179 P 0.000244
1375422_at 23049 P 0.000244
1398830_at 22142 P 0.000244
1367717_at 21932.4 P 0.000244
1367661_at 21781.1 P 0.000244
1368211_at 21318.9 P 0.000244
1375219_a_at 21288.5 P 0.000244

Total number of rows: 15923

Table truncated, full table size 427 Kbytes.




Supplementary file Size Download File type/resource
GSM81022.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM81022.EXP.gz 585 b (ftp)(http) EXP

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