Peripheral blood DNA transcriptomics of ustekinumab treatment response in patients with Crohn's disease
Data pertains longitudinal transcriptomic data measured from blood obtained from patients with Crohn's disease that were starting treatment with ustekinumab. Samples were obtained prior to treatment and approximately 26 weeks into treatment during response assessment. At response assessment, patients were classified as responders (R) or non-responders (NR) based on a strict combination of endoscopic, biochemical and clinical criteria: ≥50% reduction in the endoscopic SES-CD score, corticosteroid-free clinical remission (≥3 point drop98 in HBI or HBI ≤4 and no systemic steroids) and/or biochemical response (C-reactive protein (CRP) and fecal calprotectin reduction ≥50% or ≤5 mg/L and fecal calprotectin ≤250 µg/g). Modified response was defined as a combination of corticosteroid-free clinical- (HBI ≤4) and biochemical (CRP ≤5 mg/L and/or fecal calprotectin ≤250 µg/g) remission between week 26-52 without treatment change through week 52. Transcriptomic analyses was conducted through RNA sequencing, wherein mRNA was extracted utilizing the QIAsymphony system, converted into cDNA and sequenced in a paired-end format on the Illumina NovaSeq6000 at the Amsterdam UMC Core Facility Genomics, generating a dataset comprising 40 million 150 bp-reads.
- 15/04/2024
- 47 samples
- DAC: EGAC50000000097
- Technology: Illumina NovaSeq 6000
Data Access Policy for the EPIC-CD data as generated by the AmsterdamUMC
Access requests undergo a comprehensive review by the Data Access Committee (DAC) of AmsterdamUMC for the EPIC-CD study. Request will only be granted to qualified users for appropriate use. Applicants are required to submit detailed proposals outlining the purpose, methodology, and ethical considerations of their research. Procedure: 1) The Applicant sends a data access request through European Genome-phenome Archive (EGA) to the DAC. 2) Upon submission, a representative of the DAC will send a Data Request Form (DRF) to the Application. Upon completing the DRF, this form must be returned to the DAC whereupon the evaluation process will commence. 3) When a request is positively evaluated, the applicant will be asked to sign the Data Sharing Agreement. Review and Conditions: - Each DRF is assessed based on the scientific profile of the applicants, the scientific merit, ethical implications, data security plans, and compliance with the relevant regulations, within a specified timeframe. - The DAC reserves the right to conduct periodic reviews to ensure responsible data use. - Approval is contingent on meeting the criteria and compliance with relevant regulations.
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| EGAS50000000263 | Epigenetics |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
| ID | File Type | Size | Located in | |
|---|---|---|---|---|
| EGAF50000093057 | fastq.gz | 3.4 GB | ||
| EGAF50000093058 | fastq.gz | 3.3 GB | ||
| EGAF50000093059 | fastq.gz | 2.2 GB | ||
| EGAF50000093060 | fastq.gz | 2.3 GB | ||
| EGAF50000093061 | fastq.gz | 3.1 GB | ||
| EGAF50000093062 | fastq.gz | 3.2 GB | ||
| EGAF50000093063 | fastq.gz | 2.4 GB | ||
| EGAF50000093064 | fastq.gz | 2.3 GB | ||
| EGAF50000093065 | fastq.gz | 3.4 GB | ||
| EGAF50000093066 | fastq.gz | 3.4 GB | ||
| EGAF50000093067 | fastq.gz | 2.5 GB | ||
| EGAF50000093068 | fastq.gz | 2.6 GB | ||
| EGAF50000093069 | fastq.gz | 2.4 GB | ||
| EGAF50000093070 | fastq.gz | 2.3 GB | ||
| EGAF50000093071 | fastq.gz | 2.5 GB | ||
| EGAF50000093072 | fastq.gz | 2.5 GB | ||
| EGAF50000093073 | fastq.gz | 2.7 GB | ||
| EGAF50000093074 | fastq.gz | 2.6 GB | ||
| EGAF50000093075 | fastq.gz | 3.0 GB | ||
| EGAF50000093076 | fastq.gz | 3.2 GB | ||
| EGAF50000093077 | fastq.gz | 2.3 GB | ||
| EGAF50000093078 | fastq.gz | 2.4 GB | ||
| EGAF50000093079 | fastq.gz | 2.2 GB | ||
| EGAF50000093080 | fastq.gz | 2.3 GB | ||
| EGAF50000093081 | fastq.gz | 2.7 GB | ||
| EGAF50000093082 | fastq.gz | 2.6 GB | ||
| EGAF50000093159 | fastq.gz | 2.2 GB | ||
| EGAF50000093160 | fastq.gz | 2.3 GB | ||
| EGAF50000093161 | fastq.gz | 2.8 GB | ||
| EGAF50000093162 | fastq.gz | 2.7 GB | ||
| EGAF50000093163 | fastq.gz | 2.7 GB | ||
| EGAF50000093164 | fastq.gz | 2.8 GB | ||
| EGAF50000093165 | fastq.gz | 2.3 GB | ||
| EGAF50000093166 | fastq.gz | 2.3 GB | ||
| EGAF50000093167 | fastq.gz | 2.8 GB | ||
| EGAF50000093168 | fastq.gz | 2.9 GB | ||
| EGAF50000093169 | fastq.gz | 2.2 GB | ||
| EGAF50000093170 | fastq.gz | 2.3 GB | ||
| EGAF50000093171 | fastq.gz | 2.2 GB | ||
| EGAF50000093172 | fastq.gz | 2.1 GB | ||
| EGAF50000093173 | fastq.gz | 3.1 GB | ||
| EGAF50000093174 | fastq.gz | 3.3 GB | ||
| EGAF50000093175 | fastq.gz | 4.1 GB | ||
| EGAF50000093176 | fastq.gz | 4.0 GB | ||
| EGAF50000093177 | fastq.gz | 2.6 GB | ||
| EGAF50000093178 | fastq.gz | 2.6 GB | ||
| EGAF50000093179 | fastq.gz | 3.8 GB | ||
| EGAF50000093180 | fastq.gz | 4.0 GB | ||
| EGAF50000093181 | fastq.gz | 3.1 GB | ||
| EGAF50000093182 | fastq.gz | 3.2 GB | ||
| EGAF50000093183 | fastq.gz | 2.8 GB | ||
| EGAF50000093184 | fastq.gz | 2.9 GB | ||
| EGAF50000093185 | fastq.gz | 3.3 GB | ||
| EGAF50000093186 | fastq.gz | 3.2 GB | ||
| EGAF50000093187 | fastq.gz | 2.8 GB | ||
| EGAF50000093188 | fastq.gz | 2.8 GB | ||
| EGAF50000093189 | fastq.gz | 5.4 GB | ||
| EGAF50000093190 | fastq.gz | 5.6 GB | ||
| EGAF50000093191 | fastq.gz | 3.2 GB | ||
| EGAF50000093192 | fastq.gz | 3.1 GB | ||
| EGAF50000093193 | fastq.gz | 4.8 GB | ||
| EGAF50000093194 | fastq.gz | 5.0 GB | ||
| EGAF50000093195 | fastq.gz | 2.2 GB | ||
| EGAF50000093196 | fastq.gz | 2.2 GB | ||
| EGAF50000093197 | fastq.gz | 214.1 MB | ||
| EGAF50000093198 | fastq.gz | 213.1 MB | ||
| EGAF50000093199 | fastq.gz | 2.2 GB | ||
| EGAF50000093200 | fastq.gz | 2.3 GB | ||
| EGAF50000093201 | fastq.gz | 2.4 GB | ||
| EGAF50000093202 | fastq.gz | 2.3 GB | ||
| EGAF50000093203 | fastq.gz | 2.3 GB | ||
| EGAF50000093204 | fastq.gz | 2.3 GB | ||
| EGAF50000093205 | fastq.gz | 2.7 GB | ||
| EGAF50000093206 | fastq.gz | 2.7 GB | ||
| EGAF50000093207 | fastq.gz | 2.7 GB | ||
| EGAF50000093208 | fastq.gz | 2.8 GB | ||
| EGAF50000093209 | fastq.gz | 2.5 GB | ||
| EGAF50000093210 | fastq.gz | 2.5 GB | ||
| EGAF50000093211 | fastq.gz | 2.2 GB | ||
| EGAF50000093212 | fastq.gz | 2.3 GB | ||
| EGAF50000093213 | fastq.gz | 3.8 GB | ||
| EGAF50000093214 | fastq.gz | 3.6 GB | ||
| EGAF50000093215 | fastq.gz | 2.6 GB | ||
| EGAF50000093216 | fastq.gz | 2.7 GB | ||
| EGAF50000093217 | fastq.gz | 3.0 GB | ||
| EGAF50000093218 | fastq.gz | 3.1 GB | ||
| EGAF50000093219 | fastq.gz | 3.1 GB | ||
| EGAF50000093220 | fastq.gz | 3.2 GB | ||
| EGAF50000093221 | fastq.gz | 2.6 GB | ||
| EGAF50000093222 | fastq.gz | 2.5 GB | ||
| EGAF50000093223 | fastq.gz | 2.8 GB | ||
| EGAF50000093224 | fastq.gz | 2.9 GB | ||
| EGAF50000093225 | fastq.gz | 2.7 GB | ||
| EGAF50000093226 | fastq.gz | 2.5 GB | ||
| 94 Files (263.0 GB) | ||||