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Sample GSM1263840 Query DataSets for GSM1263840
Status Public on Nov 11, 2014
Title BcA86, biological replicate 2
Sample type RNA
 
Source name BcA86 whole lung tissue
Organism Mus musculus
Characteristics strain: BcA86
tissue: whole lung
Treatment protocol All animals were naïve and untreated.
Growth protocol All animals were house in a specific pathogen free facility in 12 hours of darkness and 12 hours of light, and with access to food and water ad libitum. Animals were sacrified by carbon dioxide overdose and lungs were collected in RNAlater stabilization reagent (Qiagen). Samples were left in RNAlater solution overnight at 4 degrees then at -80 degrees for long term storage. Lungs were collected from three different mice for each strain.
Extracted molecule total RNA
Extraction protocol All RNA samples were extracted at the same time in the same manner using the RNeasy mini kit (Qiagen) following the manufacturer's protocol.
Label biotin
Label protocol cRNA was created using the Ambion WT expression Kit (Affymetrix) and cRNA was labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix) following the manufacturer's instructions.
 
Hybridization protocol Hybridization of cartidge arrays was done using the Gene-Chip Hybridization, Wash and Stain Kit (Affymetrix) following the manufacturer's instructions.
Scan protocol Followng hybridization gene chip was processed with the Hybridization Wash and Stain Kit (Affymetrix) following the manufacturer's instructions. Arrays were scanned using Affymetrix GeneChip Scanner 3000.
Description Gene expression data from mouse whole lung tissue
Data processing Raw data was analyzed using the FlexArray software (McGill University). Data was normalized by Robust Multi-array Average (RMA) method for ST array. Strains were compared by cyber-T test and markers were deemed as significant if their fold change was <0.71 or >1.4 and p<0.05.
 
Submission date Nov 13, 2013
Last update date Nov 11, 2014
Contact name Cynthia Kanagaratham
E-mail(s) cynthia.kanagaratham@mail.mcgill.ca
Organization name McGill University
Department Human Genetics
Lab Danuta Radzioch
Street address 1650 Cedar Ave.
City Montreal
State/province Quebec
ZIP/Postal code H3G 1A4
Country Canada
 
Platform ID GPL16570
Series (1)
GSE52356 Mapping of a QTL for airway hyperresponsiveness on mouse chromosome 12

Data table header descriptions
ID_REF
VALUE Values reported for each probeset are log2 of expression values after RMA normalization.

Data table
ID_REF VALUE
17200001 6.955009025
17200003 6.353034247
17200005 5.153183034
17200007 4.918643759
17200009 5.465317063
17200011 5.590489123
17200013 5.694846477
17200015 6.04371382
17200017 2.596434684
17200019 5.443157018
17200021 5.618940747
17200023 7.455776717
17200025 6.521708355
17200027 6.750959555
17200029 4.793598192
17200031 4.064021071
17200033 5.602757578
17200035 6.320955874
17200037 5.733347743
17200039 4.233686554

Total number of rows: 41345

Table truncated, full table size 843 Kbytes.




Supplementary file Size Download File type/resource
GSM1263840_6_DRH304-3_01.CEL.gz 9.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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