Gene Expression
Nebulas
Gene Expression NebulasSummary: RNA sequencing was performed on RNA isolated from baseline biopsies from UC patients enrolled in the Phase II EUCALYPTUS study of etrolizumab. Gene expression differences were identified in a subset of anti-TNF naive patients that achieved clinical remission at 10 weeks in response to etrolizumab.
Overall Design: Baseline colonic biopsies from UC patients treated with etrolizumab were sequenced by the Illumina HiSeq 2000 Sequencing System.
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| Growth Protocol: | - |
| Treatment Protocol: | 10 weeks after etrolizumab |
| Extract Protocol: | RNAlater biopsies were homogenized using Tissuelyzer (Qiagen, Hilden, Germany) and ribonucleic acid (RNA) was isolated using the RNeasy® Mini Kit (Qiagen, Hilden, Germany) according to manufacturer instructions. |
| Library Construction Protocol: | Total RNA (RNA integrity number > 5; 250 ng) was put into the Illumina TruSeq RNA Sample Preparation Kit v2 protocol and run in conjunction with Biomek liquid handling platforms (Beckman Coulter Life Sciences). RNA libraries were evaluated using the Agilent 2200 TapeStation HighSensitivity D1K Tape and quantitative polymerase chain reaction (qPCR) with the KAPA Library Quantification Kit for Illumina sequencing. 2 nM of library (12 samples per lane) was loaded for cluster generation and sequenced on the Illumina HiSeq 2000 Sequencing System at 2 × 50 base pairs read length plus index read. |
| Molecule Type: | poly(A)+ RNA |
| Library Source: | |
| Library Layout: | PAIRED |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2000 |
| 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 |
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