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• DNA from colon cancer samples and matched normal samples was hybridized on Human 660W-Quad SNP arrays and sequenced in Illumina HiScanSQ.

  DNA from colon cancer samples and matched normal samples was hybridized on Human 660W-Quad SNP arrays and sequenced in Illumina HiScanSQ. The objective of the study was to introduce methodology for the detection of genomic copy number alterations (CNAs) using high-throughput sequencing data. The samples in this study allow the comparison of the results from the seqCNA R package with those from other methods that detect copy number alterations (CNAs) in tumoural samples, either using SNP-array data or high-throughput sequencing data.

  Study EGAS00001000558

• The aim of this study was to identify underlying hub genes and dysregulated pathways associated with the development of HCC using bioinformatics analysis.

  In the present study, we identified differentially expressed protein-coding genes from RNA transcriptional profiling performed on 11 paired cancer tissues and adjacent non-cancerous tissues. Then, we conducted GO, KEGG, PPI network and centralities analyses to study and identify changes in pathways and hub genes. The aim of this study was to improve understanding of HCC carcinogenesis by providing information concerning the genetic changes that occur during disease progression and to uncover the expression of biomarkers with potential use for clinical diagnosis, treatment, and monitoring of disease progression.

  Study EGAS00001002526

• WGS data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

  WGS data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

  Dataset EGAD00001008646

• WTCCC case-control study for Inflammatory Bowel Disease, T1D and RA - combined cases

  WTCCC genome-wide case-control association study using three disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000008

• Whole exome sequencing of pretreatment gastric and gastroesophageal junction tumors

  This set contains 40 bam files with whole exome sequencing data from 20 patients included in the PANDA study treated with 1 cycle of monotherapy atezolizumab and 4 cycles atezolizumab plus chemotherapy (docetaxel, oxaliplatin and capecitabine). Tumor DNA was isolated from tumor samples and germline DNA was isolated from PBMCs, which was used for whole exome sequencing.

  Dataset EGAD50000000242

• Malagasy Genomics University of Antananarivo Dataset

  Mid-pass whole genome sequencing was performed for 264 Malagasy individuals across three geographic regions across the island of Madagascar (west coast, central highlands, and southern highlands). This dataset includes the VCF from joint variant calling with reference populations as specified in the associated publication.

  Dataset EGAD50000000708

• Dataset for Multiple Myeloma RNA data

  This dataset contains 371 case and control RNA sequencing samples of patients with multiple myeloma. Sequencing was performed on Illumina NovaSeq 6000 and HiSeq X, HiSeq 4000 and HiSeq 2000 using TruSeq Stranded RNA and TruSeq Stranded total mRNA Kits. The sequencing was always paired.

  Dataset EGAD50000000683

• DNA methylation changes associated with hyperglycemia in type 1 diabetes

  This dataset includes DNA methylation profiles from 112 young with Type 1 Diabetes (T1D) at T1D diagnosis, who were longitudinally monitored for hyperglycemia over an average duration of 3 years. These datasets were generated using whole-genome bisulfite sequencing. It includes 1872 fastq files (i.e. 936 paired-end fastq files) generated through 150 bp paired-end sequencing on Illumina HiSeqX.

  Dac EGAC50000000237

• ResolveCRPS study - Transcriptomics

  Transcriptome profiling of CRPS-affected skin using low-input total RNA-seq (paired-end mode with 54 and 68 nt read length for R1 and R2 respectively, Illumination NextSeq2000). 42 snap-frozen skin biopsies were analyzed together with longitudinal clinical data. The dataset contains FASTQ files, the processed read count matrix, and the corresponding clinical metadata.

  Dataset EGAD50000001545

• Spatial Dynamics of the Developing Human Heart

  68 paired-end raw FASTQ files obtained from 38 tissue sections across 16 hearts, spanning embryonic human heart development between 5.5 and 14 postconceptional weeks. Some libraries were re-sequenced for better coverage. The tissue sections were processed using the 10x Genomics Visium Gene Expression kit, and libraries were paired-end sequenced using Nextseq2000 (Illumina).

  Dataset EGAD50000001615