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Sample GSM1152265 Query DataSets for GSM1152265
Status Public on Sep 11, 2014
Title Whole trachea WT, PND 0, biological replicate 1
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 2370, 2374)
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 6.81124
10411593 4.01078
10351644 4.27236
10461553 4.56512
10436128 4.01222
10411595 4.50654
10485979 3.82653
10545940 6.44469
10521515 5.32228
10486081 4.86558
10595900 6.50893
10485982 10.5679
10606001 6.71036
10461558 5.41963
10411609 9.73461
10595892 4.09641
10571467 8.03777
10411611 4.59863
10595895 4.55882
10546047 4.75584

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM1152265_Trachea_WT_PND0_rep1_43.CEL.gz 4.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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