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-Tg males (animal numbers 22818, 2886, 2887, 2888)
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
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.
