Gene Expression
Nebulas
Gene Expression NebulasSummary: Samples were obtained as part of a randomized, double blind, placebo-controlled, phase IIb study to determine the effects of myo-inositol in smokers with bronchial dysplasia. Smokers with greater than 1 site of dysplasia identified by autofluorescence bronchoscopy-directed biopsy were randomly assigned to receive oral placebo or myo-inositol, 9 g once/day for two weeks and then twice/day for 6 months. Cytologically normal airway epithelial cells were obtained via bronchoscopy from the right or left mainstem bronchus at baseline and 6 months post-treatment with myo-inositol or placebo from 69 study participants (n=138 samples). The RNA from these samples was isolated and used to prepare libraries for mRNA sequencing. Subjects were classified by response according to their change in dysplasia rate after 6-months. Among subjects with a complete response in the myo-inositol arm, there was a significant decrease in a gene expression signature reflective of PI3K activation.
Overall Design: Cytologically normal bronchial airway cells were profiled by mRNA-Seq from 69 phase IIb study participants with bronchial dysplasia before and after 6 months of treatment with oral placebo or myo-inositol.
| Strategy: |
|
| Species: |
|
| Tissue: |
|
| Healthy Condition: |
|
| Cell Type: |
|
| Growth Protocol: | - |
| Treatment Protocol: | arm: Placebo; arm: Myo-Inositol |
| Extract Protocol: | The libraries were multiplexed in groups of six using the Illumina® TruSeq® Paired-End Cluster Kit. Each sample was sequenced on an Illumina® HiSeq® 2500 to generate paired-end 100-nucleotide reads. |
| Library Construction Protocol: | Total RNA was extracted using the miRNeasy Mini Kit (QIAgen)." "Total RNA was extracted using the miRNeasy Mini Kit (QIAgen)." "Total RNA was extracted using the miRNeasy Mini Kit (QIAgen). |
| Molecule Type: | poly(A)+ RNA |
| Library Source: | |
| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| Strand-Specific: | Unspecific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
|---|