About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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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.

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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 Quality Report
Located in
i
EGAF50000093057 fastq.gz 3.4 GB Report
EGAF50000093058 fastq.gz 3.3 GB Report
EGAF50000093059 fastq.gz 2.2 GB Report
EGAF50000093060 fastq.gz 2.3 GB Report
EGAF50000093061 fastq.gz 3.1 GB Report
EGAF50000093062 fastq.gz 3.2 GB Report
EGAF50000093063 fastq.gz 2.4 GB Report
EGAF50000093064 fastq.gz 2.3 GB Report
EGAF50000093065 fastq.gz 3.4 GB Report
EGAF50000093066 fastq.gz 3.4 GB Report
EGAF50000093067 fastq.gz 2.5 GB Report
EGAF50000093068 fastq.gz 2.6 GB Report
EGAF50000093069 fastq.gz 2.4 GB Report
EGAF50000093070 fastq.gz 2.3 GB Report
EGAF50000093071 fastq.gz 2.5 GB Report
EGAF50000093072 fastq.gz 2.5 GB Report
EGAF50000093073 fastq.gz 2.7 GB Report
EGAF50000093074 fastq.gz 2.6 GB Report
EGAF50000093075 fastq.gz 3.0 GB Report
EGAF50000093076 fastq.gz 3.2 GB Report
EGAF50000093077 fastq.gz 2.3 GB Report
EGAF50000093078 fastq.gz 2.4 GB Report
EGAF50000093079 fastq.gz 2.2 GB Report
EGAF50000093080 fastq.gz 2.3 GB Report
EGAF50000093081 fastq.gz 2.7 GB Report
EGAF50000093082 fastq.gz 2.6 GB Report
EGAF50000093159 fastq.gz 2.2 GB Report
EGAF50000093160 fastq.gz 2.3 GB Report
EGAF50000093161 fastq.gz 2.8 GB Report
EGAF50000093162 fastq.gz 2.7 GB Report
EGAF50000093163 fastq.gz 2.7 GB Report
EGAF50000093164 fastq.gz 2.8 GB Report
EGAF50000093165 fastq.gz 2.3 GB Report
EGAF50000093166 fastq.gz 2.3 GB Report
EGAF50000093167 fastq.gz 2.8 GB Report
EGAF50000093168 fastq.gz 2.9 GB Report
EGAF50000093169 fastq.gz 2.2 GB Report
EGAF50000093170 fastq.gz 2.3 GB Report
EGAF50000093171 fastq.gz 2.2 GB Report
EGAF50000093172 fastq.gz 2.1 GB Report
EGAF50000093173 fastq.gz 3.1 GB Report
EGAF50000093174 fastq.gz 3.3 GB Report
EGAF50000093175 fastq.gz 4.1 GB Report
EGAF50000093176 fastq.gz 4.0 GB Report
EGAF50000093177 fastq.gz 2.6 GB Report
EGAF50000093178 fastq.gz 2.6 GB Report
EGAF50000093179 fastq.gz 3.8 GB Report
EGAF50000093180 fastq.gz 4.0 GB Report
EGAF50000093181 fastq.gz 3.1 GB Report
EGAF50000093182 fastq.gz 3.2 GB Report
EGAF50000093183 fastq.gz 2.8 GB Report
EGAF50000093184 fastq.gz 2.9 GB Report
EGAF50000093185 fastq.gz 3.3 GB Report
EGAF50000093186 fastq.gz 3.2 GB Report
EGAF50000093187 fastq.gz 2.8 GB Report
EGAF50000093188 fastq.gz 2.8 GB Report
EGAF50000093189 fastq.gz 5.4 GB Report
EGAF50000093190 fastq.gz 5.6 GB Report
EGAF50000093191 fastq.gz 3.2 GB Report
EGAF50000093192 fastq.gz 3.1 GB Report
EGAF50000093193 fastq.gz 4.8 GB Report
EGAF50000093194 fastq.gz 5.0 GB Report
EGAF50000093195 fastq.gz 2.2 GB Report
EGAF50000093196 fastq.gz 2.2 GB Report
EGAF50000093197 fastq.gz 214.1 MB Report
EGAF50000093198 fastq.gz 213.1 MB Report
EGAF50000093199 fastq.gz 2.2 GB Report
EGAF50000093200 fastq.gz 2.3 GB Report
EGAF50000093201 fastq.gz 2.4 GB Report
EGAF50000093202 fastq.gz 2.3 GB Report
EGAF50000093203 fastq.gz 2.3 GB Report
EGAF50000093204 fastq.gz 2.3 GB Report
EGAF50000093205 fastq.gz 2.7 GB Report
EGAF50000093206 fastq.gz 2.7 GB Report
EGAF50000093207 fastq.gz 2.7 GB Report
EGAF50000093208 fastq.gz 2.8 GB Report
EGAF50000093209 fastq.gz 2.5 GB Report
EGAF50000093210 fastq.gz 2.5 GB Report
EGAF50000093211 fastq.gz 2.2 GB Report
EGAF50000093212 fastq.gz 2.3 GB Report
EGAF50000093213 fastq.gz 3.8 GB Report
EGAF50000093214 fastq.gz 3.6 GB Report
EGAF50000093215 fastq.gz 2.6 GB Report
EGAF50000093216 fastq.gz 2.7 GB Report
EGAF50000093217 fastq.gz 3.0 GB Report
EGAF50000093218 fastq.gz 3.1 GB Report
EGAF50000093219 fastq.gz 3.1 GB Report
EGAF50000093220 fastq.gz 3.2 GB Report
EGAF50000093221 fastq.gz 2.6 GB Report
EGAF50000093222 fastq.gz 2.5 GB Report
EGAF50000093223 fastq.gz 2.8 GB Report
EGAF50000093224 fastq.gz 2.9 GB Report
EGAF50000093225 fastq.gz 2.7 GB Report
EGAF50000093226 fastq.gz 2.5 GB Report
94 Files (263.0 GB)