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Sample GSM476218 Query DataSets for GSM476218
Status Public on Nov 30, 2010
Title mouse659-lungs-C57BL/6J Treated-rep-1
Sample type RNA
 
Source name C57BL/6J Treated
Organism Mus musculus
Characteristics gender: male
tissue: whole lung
strain: C57BL/6J
Treatment protocol Control mice were i.p. sensitized with 10 ug Der p 1 on days 1 and 8, then challenged with PBS on day 15. Treated mice were i.p. sensitized with 10 ug Der p 1 days 1 and 8 and then challenged with 50 ug Der p 1 on day 15. All mice were harvested on day 18 (72 hours after challenge).
Growth protocol The right lower lobe was inflated with OCT and then flash frozen in liquid nitrogen.
Extracted molecule total RNA
Extraction protocol Lung lobes were homogenized and then RNA was isolated using RNeasy Mini Kits (Qiagen), according to the manufacturer’s instructions. RNAs were DNAseI treated, then rRNAs were removed using Invitrogen RiboMinus kits.
Label biotin
Label protocol RNA quality and quantity was ensured using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc) respectively. Per RNA labeling, 1 microgram of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip® WT Sense Target Labeling. The total RNA was first subjected to a ribosomal RNA reduction using the Invitorgen RiboMinus Transcriptome Isolation Kit (catalog# K1550-01). The remaining rRNA striped RNA is reverse transcribed in the presence of T7(N6) primers and a double stranded cDNA is generated. An In Vitro Transcription is performed and the resulting cRNA is purified. A first strand cDNA is generated form the cRNA in the presence of dUTPs. After RNA hydrolysis, the single stranded cDNA is fragmented and end labeled with Biotin.
 
Hybridization protocol The hybridization cocktail containing the fragmented and Biotin labeled cDNAs were hybridized to The Affymetrix GeneChip® Mouse Exon 1.0 ST Array. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).
Scan protocol An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using the Affymetrix Expression Console software and the Cel files generated.
Description RMA expression value derived from Partek Genomics Suite software; core-exon analysis
Data processing Raw data were processed and analyzed using Partek Genomics Suite Software. Core-exon analysis was used and then gene-level estimates of expression were calculated.
 
Submission date Nov 30, 2009
Last update date Nov 30, 2009
Contact name Christopher Pan
E-mail(s) cpan@mail.nih.gov
Organization name NIH
Department NHGRI
Street address Rm 5228, Bldg 50, South Dr.
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL6096
Series (1)
GSE19223 Strain-dependent Dissociation of Airway Hyper-responsiveness from Inflammation in a House Dust Mite Model of Asthma

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
6823768 7.99236
6958212 4.83953
6933677 7.28805
6933678 7.95075
6933679 9.1255
6983639 6.8184
6958216 8.89026
6873744 8.17936
6763840 3.5718
6763841 5.51222
6933697 6.61864
6958232 4.07152
6788368 8.86895
6898276 6.43311
6823797 4.70982
6823798 3.90066
6788375 4.74806
6763853 6.20084
6823813 4.98756
6788380 7.31316

Total number of rows: 16715

Table truncated, full table size 259 Kbytes.




Supplementary file Size Download File type/resource
GSM476218_SK_08-C57BL6J_659.CEL.gz 22.0 Mb (ftp)(http) CEL
GSM476218_SK_08-C57BL6J_659.rma-gene-core.chp.gz 174.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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