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Peripheral blood DNA transcriptomics of vedolizumab 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 vedolizumab. 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.

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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
EGAF50000093083 fastq.gz 3.2 GB
EGAF50000093084 fastq.gz 3.1 GB
EGAF50000093085 fastq.gz 2.9 GB
EGAF50000093086 fastq.gz 2.8 GB
EGAF50000093087 fastq.gz 2.9 GB
EGAF50000093088 fastq.gz 2.7 GB
EGAF50000093089 fastq.gz 3.0 GB
EGAF50000093090 fastq.gz 2.9 GB
EGAF50000093091 fastq.gz 3.5 GB
EGAF50000093092 fastq.gz 3.3 GB
EGAF50000093093 fastq.gz 3.1 GB
EGAF50000093094 fastq.gz 3.3 GB
EGAF50000093095 fastq.gz 2.8 GB
EGAF50000093096 fastq.gz 2.8 GB
EGAF50000093097 fastq.gz 3.5 GB
EGAF50000093098 fastq.gz 3.4 GB
EGAF50000093099 fastq.gz 2.3 GB
EGAF50000093100 fastq.gz 2.3 GB
EGAF50000093101 fastq.gz 3.5 GB
EGAF50000093102 fastq.gz 3.4 GB
EGAF50000093103 fastq.gz 3.3 GB
EGAF50000093104 fastq.gz 3.3 GB
EGAF50000093105 fastq.gz 3.1 GB
EGAF50000093106 fastq.gz 3.1 GB
EGAF50000093107 fastq.gz 3.0 GB
EGAF50000093108 fastq.gz 3.1 GB
EGAF50000093109 fastq.gz 2.9 GB
EGAF50000093110 fastq.gz 2.9 GB
EGAF50000093111 fastq.gz 3.0 GB
EGAF50000093112 fastq.gz 2.9 GB
EGAF50000093113 fastq.gz 2.8 GB
EGAF50000093114 fastq.gz 2.7 GB
EGAF50000093115 fastq.gz 3.3 GB
EGAF50000093116 fastq.gz 3.4 GB
EGAF50000093117 fastq.gz 3.1 GB
EGAF50000093118 fastq.gz 3.1 GB
EGAF50000093119 fastq.gz 2.4 GB
EGAF50000093120 fastq.gz 2.5 GB
EGAF50000093121 fastq.gz 2.7 GB
EGAF50000093122 fastq.gz 2.6 GB
EGAF50000093123 fastq.gz 3.2 GB
EGAF50000093124 fastq.gz 3.2 GB
EGAF50000093125 fastq.gz 2.6 GB
EGAF50000093126 fastq.gz 2.6 GB
EGAF50000093127 fastq.gz 3.0 GB
EGAF50000093128 fastq.gz 2.9 GB
EGAF50000093129 fastq.gz 2.8 GB
EGAF50000093130 fastq.gz 2.7 GB
EGAF50000093131 fastq.gz 3.0 GB
EGAF50000093132 fastq.gz 3.0 GB
EGAF50000093133 fastq.gz 2.4 GB
EGAF50000093134 fastq.gz 2.4 GB
EGAF50000093135 fastq.gz 3.6 GB
EGAF50000093136 fastq.gz 3.5 GB
EGAF50000093137 fastq.gz 2.8 GB
EGAF50000093138 fastq.gz 2.7 GB
EGAF50000093139 fastq.gz 2.1 GB
EGAF50000093140 fastq.gz 2.2 GB
EGAF50000093141 fastq.gz 2.6 GB
EGAF50000093142 fastq.gz 2.7 GB
EGAF50000093143 fastq.gz 3.4 GB
EGAF50000093144 fastq.gz 3.4 GB
EGAF50000093145 fastq.gz 2.8 GB
EGAF50000093146 fastq.gz 2.8 GB
EGAF50000093147 fastq.gz 3.4 GB
EGAF50000093148 fastq.gz 3.4 GB
EGAF50000093149 fastq.gz 5.8 GB
EGAF50000093150 fastq.gz 5.6 GB
EGAF50000093151 fastq.gz 3.1 GB
EGAF50000093152 fastq.gz 3.0 GB
EGAF50000093153 fastq.gz 7.5 GB
EGAF50000093154 fastq.gz 7.5 GB
EGAF50000093155 fastq.gz 2.5 GB
EGAF50000093156 fastq.gz 2.5 GB
EGAF50000093157 fastq.gz 2.8 GB
EGAF50000093158 fastq.gz 2.7 GB
76 Files (237.9 GB)