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Sample GSM1152281 Query DataSets for GSM1152281
Status Public on Sep 11, 2014
Title Whole trachea Scnn1b-T, PND 3, biological replicate 2
Sample type RNA
 
Source name Scnn1b-Tg, trachea
Organism Mus musculus
Characteristics strain: C57Bl/6N Tac
genotype: Scnn1b-Transgenic
age (postnatal day): 3
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 post natal day 3 Scnn1b-transgenic males (animal numbers 2783, 2784, 2785)
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 6.4927
10411593 4.13139
10351644 4.4744
10461553 4.80014
10436128 4.22401
10411595 4.84192
10485979 3.76597
10545940 6.31054
10521515 5.10436
10486081 5.32768
10595900 6.83113
10485982 8.98181
10606001 7.02015
10461558 5.20275
10411609 9.77493
10595892 4.19454
10571467 6.69728
10411611 4.7786
10595895 4.84928
10546047 5.16071

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM1152281_Trachea_Scnn1b-Tg_PND3_rep2_35.CEL.gz 3.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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