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• 20210708_EGA_Melanoma_mk2 WGS 570 donors

  Illumina platform whole genome sequencing data for matched tumour-normal DNA samples from 570 melanoma patients

  Dataset EGAD00001008798

• scRNAseq from MPNST progression

  scRNAseq from tumors of the peripheral nerve system associated with Neurofibromatosis Type 1 (NF1). It includes 5 Plexiform Neurofibromas (PNF), 4 Atypical Neurofibromas (ANF or ANNUBP) and 3 Malignant Peripheral Nerve Sheath Tumors (MPNST) from patients with NF1 as well as 4 control nerves from healthy individuals. Gene Expression data from 10X scMultiome experiments.

  Dataset EGAD50000002508

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set4)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of one hyperdiploid ALL patient (ALLK-134). Sequencing libraries were made using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq X Plus.

  Dataset EGAD50000002429

• Whole genome sequencing data of pediatric hypodiploid B cell acute lymphoblastic leukemia

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) bone marrow samples of one hypodiploid ALL patient (ALLT-351). Sequencing library was made using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000001856

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set6)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of one B-other ALL patients (ALLK-138). Sequencing library was made using Novogene NGS DNA Library Prep Set. Both diagnostic (90x) and remission (30x) samples were sequenced using NovaSeqX Plus.

  Dataset EGAD50000002161

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set4)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of two B-other ALL patients (ALLT-389, ALLK-124). Sequencing library was made using Novogene NGS DNA Library Prep Set. Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002159

• RNA sequencing of 120 AML samples

  This dataset contains fastq-files from bulk RNA sequencing of 120 AML samples. RNA was extracted from either bone marow or peripheral blood from primary AML samples. The libraries were prepared using Illumina Truseq RNA library preparation kit v2 and sequenced on an Illumina NextSeq 500 using 2x151bp paired end chemistry.

  Dataset EGAD50000001576

• Single-cell RNA-sequencing on malignant and benign tissue samples

  Single-cell RNA-sequencing on malignant and benign tissue samples from untreated donors with colorectal adenocarcinoma and liver metastasis was performed in order to deduce tissue adaptive expression patterns of the disease. Matching tissue from five donors with untreated CRC and liver metastasis were sampled.

  Dataset EGAD50000001203

• Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer

  Dataset with eQTL and e2QTL metadata. The analyses were performed using CD8+ T cells from 461 healthy European participants stimulated with high doses of 5 different carcinogens to induce early apoptosis. These include Methyl-methanesulfonate (MMS), tert-butyl-hydroperoxide (TBOOH), benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE), 4-hydroxycyclophosphamide (HC) and UVC radiation.

  Dataset EGAD50000000941

• Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing

  In this study, we analyzed 28 primary cutaneous follicle center lymphoma samples from 20 patients and compared the copy number profiles to a cohort of diagnostic samples of 64 nodal follicular lymphoma patients using low-coverage whole genome sequencing (lcWGS).

  Dataset EGAD50000000199

• Transcriptome atlas of brain organoid developent

  Single-cell Cut&Tag of three histone modifications and chromatin accessibility over a timecourse of brain organoid development from pluripotency. We profiled 5 time points of brain organoid development and 2 time points of retinal organoid development. We used scRNA-seq to profile transcriptome. Library preparation was carried out with the 10x genomics platform.

  Dataset EGAD50000000223

• Heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer

  A mutation accumulation experiment in colorectal cancer (CRC) derived tumoroids. A sequential single-cell cloning approach was adopted to measure the mutation rate in eight tumoroids obtained from five patients. WGS was also performed on their matched normal tissue and on standard tumoroids cultures without any cloning step.

  Dataset EGAD50000000411

• Mutational consequences of precancerous liver disease

  Clonally expanded liver adult stem cell clones of healthy liver and cirrhotic liver (due to alcohol abuse, NASH and PSC), as well as biopsies of liver cancers were subjected to whole genome sequencing to determine the mutational impact of precancerous liver disease

  Dataset EGAD00001004105

• H3K27ac ChiIP-seq of monocyte and granulocytes from TB and non-TB samples

  This dataset contains 135 H3K27ac ChiP-seq experiments. Monocytes and granulocytes from TB and non-TB samples were obtained, ChIP-seq was performed, and the reads were aligned to hg19.

  Dataset EGAD00001004206

• Triple Negative BC WGS Dataset

  We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Dataset EGAD00001001335

• Triple Negative Breast Cancer Whole Genome Validations

  We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. This study will use a bespoke bait set to pulldown regions of interest found in whole genome sequencing to validate mutations found.

  Dataset EGAD00001000662

• Exome sequencing of serially transplanted genetically marked IC-enriched primary PDAC cultures.

  In order to elucidate whether newly acquired genetic alterations during serial transplantation of patient derived primary pancreatic cancer cultures contribute to the observed clonal dynamics in vivo, all coding genes of two patient derived primary cultures and derived genetically marked serial xenografts (1°/2°/3°) were sequenced.

  Dataset EGAD00001000884

• IBD WES trio data-ALPI-P2

  This project focused on identifying rare coding variation that substantially increases risk of VEOIBD by exome sequencing of VEOIBD patients and some of their family members. Here you can find BAM files from an affected proband (P2) and his unaffected parents. In this study ALPI mutations were identified as a likely cause of the disease.

  Dataset EGAD00001004485

• WGBS analysis corresponding to representative cases of iBCP-ALL patients

  This dataset was conceived to characterize the epigenomic landscape of representative iBCP-ALL subtypes. To do so, we performed Whole Genome DNA bisulfite-sequencing on 2 MLL-AF4, 2 MLL-AF9 and 2 non-MLL rearranged leukemias, and also 2 pools of BCPs obtained from fetal liver.

  Dataset EGAD00001005010

• cfDNA mutation analysis using TAPAS in plasma and urine

  A 2.077Mb (57306 probes) personalised capture panel [Tailored Panel Sequencing (TAPAS)] was designed based upon the somatic SNVs identified by WES of RCC patient FF and FFPE tissue samples and applied to cfDNA in plasma and urine.

  Dataset EGAD00001005813

• Whole genome sequencing of patient IPSCs and tumors (organoids)

  This dataset contains whole genome sequencing data of a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) . This dataset further contains whole genome sequencing data of two tumors showing CNLOH. Tumors were isolated from organoids grown using the patient IPS cell line (Patient 1 TSC2+/- iPSCs )

  Dataset EGAD00001006333

• Sequence of breast cancer bone metastases PDX before and after palbociclib treatment resistance

  RNAseq sequencing of 10 breast cancer bone metastasis PDX. Samples were obtained from 5 PDX that acquired palbociclib resistance (palboR) and 5 from the parentale PDX (palboS).

  Dataset EGAD00001009068

• Oropharyngeal Squamous Cell Carcinoma Mutanome

  This dataset comprises genetic variation data (as somatic indels and snvs VCFs) of 38 OPSCC tumors. WES was done using NextSeq 500 System running in 150 cycles (2x 75bp paired-end) mode. Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422. VCFs were generated using the Strelka package.

  Dataset EGAD00001009167

• RNA sequencing

  RNAseq of 45 high-grade serous ovarian cancer tumour samples. Libraries were generated using the NEB Ultra II Directional RNA library Prep kit with polyA enrichment. Libraries were sequenced as paired-end 50 or 100bp on an Illumina NextSeq or NovaSeq.

  Dataset EGAD00001009844

• Germline variants in childhood melanoma

  Whole-exome sequencing was performed on DNA extracted from blood samples of 50 children diagnosed with cutaneous melanoma prior to 18 years of age. Patients were all diagnosed in Queensland, Australia, and self-reported as of European descent. Sequencing was done the Illumina platform using SureSelct V7 Post capture kits.

  Dataset EGAD00001010039