Gene Expression
Nebulas
Gene Expression NebulasSummary: To gain a deeper understanding of the pathophysiology of AD, we conducted a large-scale transcriptomic study of AD with deeply-sequenced RNA-seq samples using long (125b) paired-end reads. By integrating deep sequencing-based skin transcriptome profiling with systems biology analysis, we are able to provide deep characterization for the expression signatures for AD, and by including psoriasis samples in the analysis, we can reveal the distinct molecular features of uninvolved and lesional skin of AD that have not been previously described.
Overall Design: We performed high-depth sequencing of 147 skin transcriptomes obtained from a carefully matched and tightly defined cohort of 27 AD patients, 28 PSO patients, and 38 healthy controls, whom were recruited within an ongoing investigator-initiated clinical study to identify shared and distinct disease mechanisms of AD and Psoriasis.
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | 5mm skin punch biopsies were stored in PaxGene tissue containers (PreAnalytiX) at -80°C until isolation of total RNA with the Qiagen AllPrep DNA/RNA Mini Kit preceded by an additional disruption/homogenization step with innuSPEED Lysis Tubes W (Analytik Jena) and Qiagen QIAshredder spin-columns. |
| Library Construction Protocol: | RNA samples were prepared for sequencing using the Illumina Truseq Stranded total RNA Protocol in combination with the RiboZero rRNA removal Kit and sequenced on the HiSeq2500 with 2x125bp. |
| Molecule Type: | poly(A)+ RNA |
| Library Source: | |
| Library Layout: | PAIRED |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| Strand-Specific: | Specific |
| 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 |
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