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Sample GSM1152266 Query DataSets for GSM1152266
Status Public on Sep 11, 2014
Title Whole trachea WT, PND 0, biological replicate 2
Sample type RNA
 
Source name Wildtype, trachea
Organism Mus musculus
Characteristics strain: C57Bl/6N Tac
genotype: Wildtype
age (postnatal day): PND 0 (<24 hrs)
Treatment protocol Not applicable; no treatment; mice are either wildtype or Scnn1b-transgenic and were harvested at post natal days 0, 3, 10, and 42.
Growth protocol Mouse whole trachea; mice grown under specific-pathogen-free conditions in micro-isolator cages
Extracted molecule total RNA
Extraction protocol Whole lungs were dissected and stored in RNALater until extraction using Qiagen RNAeasy columns, followed by ethanol precipitation
Label biotin
Label protocol RNAs were processed for hybridization to Affymetrix Mouse Gene ST 1.0 microarrays using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit and Ambion WT Expression Kit, according to manufacturer's recommended protocol.
 
Hybridization protocol Affymetrix GeneChip Hybridization Oven 640 for 16 hours at 45 degrees. Washing and staining was performed in the Affymetrix GeneChip Fluidics Station 450, protocol FS450_0007.
Scan protocol Affymetrix GeneChip Scanner 3000 7G
Description whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively); pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2377, 2410)
Data processing CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets. PND10 samples were further adjusted through Batchremoval by comparing to the rest of the samples.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps
 
Submission date May 31, 2013
Last update date Sep 12, 2014
Contact name Hong Dang
E-mail(s) dangh@email.unc.edu
Organization name UNC Chapel Hill
Department CF Center
Street address 7027 Thurston-Bowles Bldg. CB#7248
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL6246
Series (2)
GSE47550 mRNA expression data from whole trachea dissected from either wild-type mice or Scnn1b-Tg mice at post-natal days 0, 3, 10, and 42
GSE47551 mRNA expression data from either wild-type mice or Scnn1b-transgenic mice at post-natal days 0, 3, 10, and 42

Data table header descriptions
ID_REF
VALUE Mean log2 intensity as gene-level expression from exon-level probesets, normalized by RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization (Partek Genomics Suite v6.5). PND10 samples were further adjusted through Batchremoval by comparison to rest of the samples.

Data table
ID_REF VALUE
10605884 6.89117
10411593 4.09778
10351644 4.23662
10461553 4.55444
10436128 4.02607
10411595 4.34572
10485979 3.8489
10545940 6.70327
10521515 5.6432
10486081 5.18078
10595900 6.38097
10485982 10.3582
10606001 7.05078
10461558 4.76437
10411609 9.67789
10595892 4.04114
10571467 7.88574
10411611 4.42825
10595895 4.70473
10546047 5.42533

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM1152266_Trachea_WT_PND0_rep2_44.CEL.gz 4.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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