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• Columbia Alzheimer's sample (white matter)

  The Columbia Alzheimer’s dataset (white matter) consists of 24 white matter individuals (12 controls, 12 cases). A total of 12,000 estimated cells from each sample were loaded on the 10x Single Cell Next GEM G Chip. cDNA libraries were prepared using the Chromium Single Cell 3’ Library and Gel Bead v3 kit according to the manufacturer’s instructions. cDNA libraries were sequenced using the Illumina NovaSeq 6000 System and NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles), aiming at a sequencing depth of minimum 30K reads/nucleus.

  Dataset EGAD00001009168

• Transcriptome profiling of three giant cell tumour of bone (GCTB) cell lines

  This dataset contains RNA-seq data of giant cell tumour of bone (GCTB) cell lines (n=3). Cell lines consist of neoplastic "stromal" cells harboring a heterozygous H3F3A p.G34W mutation. RNA-seq was performed on the BGISEQ-500 platform (PE100) and uploaded data contains fastq files, vcf files, and gene expression values (TPM). Cell lines, data generation, and data analysis are described in the following publication: Venneker et al., Histone deacetylase inhibitors as a therapeutic strategy to eliminate neoplastic “stromal” cells from giant cell tumors of bone, 2022.

  Dataset EGAD00001009074

• IntEnd study

  Formalin-fixed, paraffin-embedded samples from 643 colorectal adenomas collected in different hospitals in Norway, from which DNA was extracted, were analysed for DNA copy number alterations. Some adenomas had more than one block (n=42), thus 643 individuals, 685 blocks. Low-coverage whole genome sequencing was run in all samples. For 529 individuals all the clinical information was available. A subset was matched for follow-up time, age and sex in a nested case-control approach (n=366; cases - individuals who developed later on CRC; controls - individuals who did not develop CRC within the same follow-up time).

  Dataset EGAD00001010119

• Targeted NGS panel

  The mutational status of 121 genes recurrently altered in B-cell lymphoma was examined in 55 of 56 diagnostic and 10 of 12 relapse samples using a custom targeted NGS panel. Libraries were generated from 150 ng of DNA using molecular-barcoded library adapters (ThruPLEX Tag- seq kit; Takara) coupled with a custom hybridization capture-based method (SureSelectXT Target Enrichment System Capture strategy, Agilent Technologies). The quality of the libraries was determined using the Bioanalyzer high sensitivity DNA kit (Agilent) and quantified by PCR using the KAPA library quantification kit (KAPA Biosystems). Finally, the libraries were pooled and sequenced in the MiSeq instrument (Illumina).

  Dataset EGAD00001010842

• Tumor and normal exomes for 95 PMBCL cases

  Whole-exome sequencing for 95 PMBCL cases (including 21 with matching normal DNA) was performed using a targeted capture approach with the SureSelect Human All Exon V6+UTR bait (Agilent Technologies) followed by massively parallel sequencing of enriched fragments on the HiSeq2500 platform (Illumina). Five libraries were pooled per lane and a 125bp paired-end mode was used. Tumor and normal DNA samples were sequenced to an average of 115X (SD 24X). All reads were aligned to the human reference genome (hg19) using bwa-mem version 0.7.5a29 with optical and PCR duplicates removed using the Picard tool.

  Dataset EGAD00001005780

• AVENIO Expanded ctDNA panel sequence alignments (BAMs) from plasma DNA of BC, CRC and NSCLC patients

  The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 48 plasma samples from patients with breast, colorectal and non-small cell lung cancer. After sequencing 150bp paired-end, reads were aligned to the hg38 genome with the AVENIO Oncology Analysis Software (version 2.0). These files are the deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling.

  Dataset EGAD00001006301

• Chracterising cellur pathways underlying CD3/CD28 activation of human CD4+ cells

  We devised an approach to disentangle the TCR and CD28 pathways upon stimulation in naive and memory primary human CD4+ T cells (Tcons) in response to defined stimulatory signals. Isolated memory and naïve T cells were activated using anti-CD3, anti-CD28 or both in combination. As a control we cultured cells in the same conditions but without the stimuli. We carried Chipmentation using the H3K27ac antibody on 200,000 cross-linked cells. 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ .

  Dataset EGAD00001006611

• DAC "Genotyping based on SNPs covered by targeted NGS"

  DAC for the dataset from the article "Genotyping from targeted NGS data based on a small set of SNPs correctly matches patient samples"

  Dac EGAC50000000358

• Plasma cell‐free transcriptome profiling in chronic liver disease

  RNAseq data from plasma samples corresponding to a Grand Challenge Programme project to find biomarkers for liver disease, including NAFLD, NASH, Cirrhosis and Hepatocelullarcarcinoma.

  Dac EGAC50000000360

• Reference epigenome SMC07_smRNA-Seq data generated from KEP study

  A SMC07_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003864

• Reference epigenome ADMSC02_ChIP-Seq(H3K27me3) data generated from KEP study

  A ADMSC02_ChIP-Seq(H3K27me3) paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003855

• Reference epigenome SMC03_smRNA-Seq data generated from KEP study

  A SMC03_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003860

• Reference epigenome SMC08_smRNA-Seq data generated from KEP study

  A SMC08_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003865

• Reference epigenome SMC09_smRNA-Seq data generated from KEP study

  A SMC09_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003866

• Reference epigenome SMC01_smRNA-Seq data generated from KEP study

  A SMC01_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003858

• Reference epigenome DB31_N_Alpha_WGBS data generated from KEP study

  A DB31_N_Alpha_WGBS paired end data for alpha cells(PSA-NCAM(-), pancreas)

  Dataset EGAD00001003472

• Reference epigenome SMC05_smRNA-Seq data generated from KEP study

  A SMC05_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003862

• Reference epigenome SMC06_smRNA-Seq data generated from KEP study

  A SMC06_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003863

• Reference epigenome ADMSC01_ChIP-Seq(H3K27me3) data generated from KEP study

  A ADMSC01_ChIP-Seq(H3K27me3) paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003854

• Reference epigenome SMC04_smRNA-Seq data generated from KEP study

  A SMC04_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003861

• CGP CORE CELL LINES - RNA-seq

  Genomic characterisation of a large series of cancer cell lines.

  Dataset EGAD00001001357

• Reference epigenome ADMSC04_ChIP-Seq(H3K27me3) data generated from KEP study

  A ADMSC04_ChIP-Seq(H3K27me3) paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003857

• Reference epigenome SMC02_smRNA-Seq data generated from KEP study

  A SMC02_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003859

• Reference epigenome ADMSC03_ChIP-Seq(H3K27me3) data generated from KEP study

  A ADMSC03_ChIP-Seq(H3K27me3) paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003856

• Reference epigenome ADMSC01_WGBS data generated from KEP study

  A ADMSC01_WGBS paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003878