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Sample GSM1227574 Query DataSets for GSM1227574
Status Public on Sep 11, 2013
Title Let1_GFP_1h.1
Sample type RNA
 
Source name immortalized airway epithelial cells, expressing GFP, infected with PR8 influenza 1 hour
Organism Mus musculus
Characteristics cell type: immortalized airway epithelial cells
transgene: GFP
time: 1 hour
infection: PR8 influenza
strain: C57BL/6
Treatment protocol Cells were infected with influenza A (A/Puerto Rico/8/34) (PR8) at MOI=5 in OptiMEM in the absence of trypsin, the inoculum removed by washing, and cells cultured in OptiMEM.
Growth protocol To generate LET1 cells, lung cells were isolated from C57Bl/6 mice using a modified dispase-agarose protocol (Herold et al., 2006), cultured to yield lung epithelial type I cells (LET1) trans-differentiated from type II epithelial cells, then immortalized by transduction with MSCV-SV40 large T antigen and used after a minimal number of passages. LET1 cells were cultured in DMEM containing 10% heat-inactivated FBS, 2 mM L-glutamine, and penicillin-streptomycin (complete DMEM), incubated at 37oC 5% CO2., passaged using a brief trypsinization, and sub-cultured 1:20 every 3 days.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from bone-marrow-derived macrophages using TRIzol (Invitrogen) according to the manufacturer's instructions. Prior to labeling, the integrity of samples was checked using an Agilent 2100 Bioanalyzer.
Label Cy3
Label protocol Labeling was performed with the One-Color Microarray-Based Gene Expression Analysis protocol version 6.5 (Agilent). Briefly, double-stranded cDNA was synthesized from 200ng of total RNA using a T7-oligo(dT) primer, followed by in vitro transcription by T7 RNA polymerase with incorporation of Cy3-labeled CTP.
 
Hybridization protocol 600ng of Cy3-labeled cRNA was hybridized in Agilent hybridization chambers for 17 hours at 65 C and 10rpm. The arrays were washed for 1 minute in Agilent GE Wash Buffer 1 and then for another minute in Agilent GE Wash Buffer 2.
Scan protocol Scanning was performed using an Agilent High-Resolution DNA Microarray Scanner, with 3 micron resolution and 20-bit dynamic range. The resulting images were processed with Agilent Feature Extraction version 10.7.3.1 to generate raw probe intensity data.
Description Gene expression in GFP expressing cells infected with PR8 influenza for 1 hour
Data processing Arrays were quantile normalized using the normalizeBetweenArrays function from the Bioconductor marray package.
 
Submission date Sep 10, 2013
Last update date Sep 11, 2013
Contact name Aderem Lab
E-mail(s) alan.diercks@seattlechildrens.org
Organization name Seattle Children's Research Institute
Lab Aderem Lab
Street address 307 Westlake Avenue North, Suite 500
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL13912
Series (1)
GSE50742 Effect of miR-144 and miR-451 expression on lung epithelial cell responses to influenza infection at 1 and 18 hours.

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensity.

Data table
ID_REF VALUE
4 29.84375
5 110.90625
6 34.1875
7 27.53125
8 2308.953125
9 38.125
10 29.84375
11 52.5625
12 34
13 335.1875
14 5453.5625
15 66.15625
16 27.53125
17 3251.90625
18 383.890625
19 1903.890625
20 64628.28125
21 222.421875
22 326.9375
23 840

Total number of rows: 59305

Table truncated, full table size 851 Kbytes.




Supplementary file Size Download File type/resource
GSM1227574_20130905_Bl6_PR8_InVitro_NonStdConc_0060_Let1a_M_GFP.1_CR_Std_.txt.gz 12.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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