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• Single-cell genotype-to-phenotype mapping via co-capture of DNA mutations and mRNA transcripts

  We developed single-cell Genotype-to-Phenotype sequencing (scG2P) for high-throughput, highly-multiplexed, single-cell joint capture of recurrently mutated genomic regions and mRNA phenotypic markers in cells or nuclei isolated from solid tissues. We applied scG2P to aged esophagus samples from five individuals with high alcohol and tobacco exposure.

  Dac EGAC50000000833

• RNAseq of 7 MPNSTs

  RNAseq of 7 MPNSTs for Magallon-Lorenz 2026. Contains 5 samples sequenced with DNBseq at BGI (four 2x100bp and one 2x150bp) and 2 samples sequenced with Illumina stranded mRNA-seq technology. BGI samples have been prefiltered with SOAPnuke. Two fastq files provided per sample with no additional filtering or QC.

  Dataset EGAD50000002493

• ChIP-seq ERa in primary breast cancer tissues

  ChIP-seq has been perfomed on 5 tumor fresh-frozen primary breast cancer tissues from female patients. Immunoprecipitation has been performed for ERa (SC-543, Santa Cruz). Raw single-end fastq data have been aligned using bwa-mem using Hg19 genome assebly as reference. Unfiltered aligment bam files are provided.

  Dataset EGAD50000000014

• Iso-seq or Long-read RNAseq Dataset for 7 T-ALL patient samples

  7 Isoform sequencing or Long-read RNAseq mapped bam files. Reads were aligned to HG38 reference using Minimap2.

  Dataset EGAD50000000022

• ATAC Dataset for 19 T-ALL patient samples and 1 normal control sample

  19 ATAC-seq from T-ALL patient samples and one healthy normal control sample. Reads were aligned to HG38 reference

  Dataset EGAD50000000024

• Sequencing data for oesophageal and related samples - BOs release 2 (RNA)

  Dataset EGAD00001003840

• EGAD00000000047

  Signal data for from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples

  Dataset EGAD00000000047

• Dataset of whole genome bisulfite data of 4 different monocyte samples

  Regions of common inter-individual DNA methylation differences in human monocytes – potential function and genetic basis WGBS Data of Samples: 43_Hm03_BlMo_Ct, 43_Hm02_BlMo_Ct, 43_Hm05_BlMo_Ct, 43_Hm01_BlMo_Ct For details about sequencing or sample metadata check http://deep.dkfz.de/

  Dataset EGAD00001003259

• 17 scRNAseq samples

  17 samples were processed for single cell RNA sequencing (SORT-seq)

  Dataset EGAD00001007523

• ctDNA dataset

  ctDNA data from IMvigor010: ctDNA data include TMB_status, cfDNA_extracted_ng, Plasma_Volume_Used_ml, Sample_Call, Sample_Number_Positive_Calls, Sample_Mean_VAF_In_Plasma (%), Sample_MTM_per_mL_In_Plasma for 581 patients across IMvigor010.

  Dataset EGAD00001007574

• Platelet RNAseq data for SLFN14 K219N patients

  RNAseq dataset containing 20 control and 2 SLFN14 K219N patient samples, derived from platelets. Sequencing libraries were constructed using an Illumina TruSeq stranded Ribo Zero Gold kit and paired end sequenced at a read depth of 30 million reads on an Illumina NovaSeq 6000 platform.

  Dataset EGAD00001008965

• 10xscRNA sequencing of 2 samples RRMM (multiple myeloma)

  Paired scRNA sequencing using 10xgenomics library preparation and Illumina HiSeq4000 for sequencing of 2 samples RRMM (relapsed refractory multiple myeloma)

  Dataset EGAD00001009681

• Longitudinal evaluation of serum microRNAs as biomarkers for neuroblastoma burden and therapeutic p53 reactivation

  Small RNA sequencing data (TruSeq small RNA library preparation kit v2) from serum samples and tumor tissue of orthotopically injected mice (SH-SY5Y cell line) and unengrafted mice, treated with idasanutlin, temsirolimus and vehicle control.

  Dataset EGAD00001009625

• Raw count matrix for 44 baseline + 44 progression samples

  Count matrix from 44 pre-treatment (Ven-Obi or Clb-Obi) and 44 paired, post-treatment relapsed CD19+ B cells.

  Dataset EGAD00001009500

• Exome sequencing data

  Libraries were constructed using SureSelect HS XT Target Enrichment System v6 (Agilent). For each patient a library of CD3- cells (myeloid cells, considered tumor cells) and CD3+ cells (T cells, considered healthy) were generated.

  Dataset EGAD00001010190

• Low-pass whole-genome DNA sequencing of cohesin-mutated and wildtype adult AMLs

  Low-pass whole-genome DNA sequencing of cohesin-mutated (STAG2 or RAD21 mutations) and wildtype (CTRL-AML) adult AMLs generated generated from ultrasound-fragmented genomic DNA. Samples were only sequenced shallow (20-40 Mio reads) Used for digital karyotyping and ChIP-seq background/copy-nuber normalization/correction.

  Dataset EGAD00001011207

• Therapeutic Targeting of ATR Yields Durable Regressions in High Replication Stress Tumors

  Patients with relapsed or recurrent small cell lung cancer or extra-pulmonary small cell cancers were enrolled on an investigator-initiated, single-arm, phase 2 trial (NCT02487095) combining an ATR inhibitor M6620 (VX-970, berzosertib) administered at 210 mg/m2 intravenously over 60 minutes on day 2 and day 5, and topotecan 1.25 mg/m2 intravenously over 30 minutes every 23 hours on days 1 through 5, with a support of pegfilgrastim 6mg subcutaneously on day 6 in 21-day cycles. Tumor samples were collected either just before starting the treatment or before starting treatment prior to be enrolled in the trial. Whole exome and RNA were sequenced to evaluate genomic and transcriptomic characteristics associated with the response to the combination treatment.

  Study phs002327

• Clonal dominance defines metastatic dissemination in pancreatic cancer

  Using patient-derived cells from a pancreatic ductal adenocarcinoma, we created orthotopic clonal replica tumors to trace in an unbiased fashion clonal lineage dynamics of unperturbed tumor expansion and dissemination over time. The model revealed the complex multifaced nature of tumor clonal expansion and uncovered brisk changes in fitness that lead to a continuous reshuffling of tumor clonal architecture and alternating clonal dominance as a distinct feature of cancer growth. Paired analysis of clonal lineages in primary and secondary sites revealed fitness in the primary tumor as a major contributor to dissemination, although other clonal intrinsic and extrinsic factors may contribute to metastatic process. Molecular characterization of lineages with differential metastatic potential identified actionable strategy to suppress dissemination at the subclonal level.

  Study EGAS00001006358

• NHLBI TOPMed - NHGRI CCDG: Penn Medicine BioBank Early Onset Atrial Fibrillation Study

  Cases with early-onset atrial fibrillation were selected from the Penn Biobank based on an age of atrial fibrillation onset prior to 61 years of age, and in the absence of a myocardial infarction, heart failure or severe valvular disease.

  Study phs001601

• 3D chromatin contacts of iPSC (controls) and mDAN (differentiated neurons) cells

  Sequencing of 3 replicates per condition to gather insights on the 3D chromatin conformation of iPCS-derived neuronal progenitors (smNPCs) and mDANs using LowC. The downstream analysis studies changes in A and B compartment interactions and in topologically associated domains (TADs).

  Study EGAS50000001578

• Identification of genetic etiology of CAMRQ2

  We aimed to identify genetic etiology of cerebellar ataxia, mental retardation, and disequilibrium syndrome (CAMRQ). Targeted sequencing of the entire CAMRQ2 locus, 7.1 Mb interval on chromosome 17p13, in three affected individuals and two obligate carriers uncovered the mutation associated with CAMRQ2.

  Study EGAS00000000099

• ICARUS-LUNG01-RNAseq

  Bulk RNA-seq was carried out on 20 pairs of frozen tumor biopsies. Differential gene expression (DGE) analyses was conducted, looking at the fold change of gene expression of matched on-T/BL samples in the overall population and, then, separately in responders and non-responders.

  Study EGAS50000000732

• 46 WES paired FASTQ germline/tumour samples from 23 early-onset prostate cancer donors from the Bob Champion Cancer Trust

  The dataset contains 46 samples: a germline and tumour sample from each of 23 donors. Donors are men diagnosed with prostate cancer at a young age, from the Bob Champion Cancer Trust. The data consists of 92 whole exome sequenced paired FASTQ files, compressed with bgzip. Exome sequences were enriched using Agilent SureSelect XT2 Human All Exon V5 baits, and sequenced with Illumina HiSeq 2500.

  Dataset EGAD50000002112

• Whole Genome Sequencing of Multiple Myeloma patients treated with T-cell redirecting immunotherapies

  Samples was collected at the Arnie Charbonneau Cancer Institute (University of Calgary). Whole Genome Sequencing was performed at the New York Genome Center, and libraries were prepared using the Truseq DNA Nano Library Preparation Kit. Libraries were sequenced on an Illumina Novaseq 6000 sequencer using 2 x 150-bp cycles. The dataset consists in 85 BAM files from patients with Multiple Myeloma treated with bi-specific and CAR-T therapies. Reference Genome: GRCh38.

  Dataset EGAD50000000776

• Primary Lung Cancer whole genome study

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from lung cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Dataset EGAD00001000388

• Mutational context and diverse clonal development in early and late bladder cancer

  Bladder cancer shows multiple recurrences probably originating from a malignant field disease in the mucosa. Deep sequencing was used on a series of tumors to look into the clonal composition, mutational spectrum in non-aggressive tumors, and mutational context.

  Study EGAS00001000641

• Targeted_sequencing_of_cylindroma_patients

  Patients with cylindroma show multiple large tumours on the scalp and forehead. These large tumours will allow us to look at clonality within a tumour. We wish to asses the mutational load and diversity within and across tumours as well as compare with perilesional skin.

  Study EGAS00001002708

• Targeted sequencing about core genes involved in telomere biology in colorectal cancer patients

  We sequenced the coding exons of core genes involved in telomere maintenance using peripheral blood DNA of 192 CRC patients. The primary sequencing data were generated by using Ion Torrent Personal Genome Machine® (PGM™) platform (Life Technologies, Carlsbad, CA, USA).

  Study EGAS00001002977

• Efficacy of CDK4/6i in preclinical models of malignant pleural mesothelioma

  Assessment of antitumor activity of CDK4/6 inhibitors using in vitro and in vivo preclinical models of MPM using RNA-sequencing. We also include the genomic characterization (whole exome sequencing) of patient-derived cell lines used in the in vitro experiments.

  Study EGAS00001005352

• WGS on patients with syndromic neurosensory disorder combining deafness and cataract

  Disease: Severe congenital deafness, early onset cataracts and various neurological features Family: 3 affected individuals originated from the same small village (Amarat) in the Kayseri region of Turkey and belonging to the same large extended consanguineous family. Dataset: 5 BAM files. Whole-genome sequencing (WGS) was applied to the three affected individuals (II.2, II.4 and II.7) and two healthy individuals (II.1 and II.3).

  Dataset EGAD00001005417

• RA-Map Early Rheumatoid Arthritis patient genotyping (InfiniumCoreExome-24-v1)

  Genotyping of 244 early RA patients and 44 vaccine recipient controls was performed using the Illumina InfiniumCoreExome-24-v1-1 according to the manufacturer’s SOP. Raw idats from the Illumina iScan instrument were imported into GenomeStudio (v2011.1). Samples < 90 % call rate were excluded. Data was exported to PLINK PED/MAP format on the forward strand. Data was converted from PED/MAP to BED/BIM/FAM using PLINK v1.07.

  Dataset EGAD00001006736

• Targeted sequencing of follicular lymphoma tumour samples from the UK's Haematological Malignancy Research Network

  Targeted sequencing was applied to an unselected population-based follicular lymphoma (FL) cohort (n=548) diagnosed in the UK's Haematological Malignancy Research Network catchment population of ~4 million (14 centres). DNA extracted from FL samples was sequenced with a 293-gene panel using the Illumina HiSeq 2500. All data are provided in the CRAM format.

  Dataset EGAD00001007657

• Single-cell RNA sequencing of erythroid and megakaryocytic acute myeloid leukemia patient cells

  Single-cell RNA sequencing was performed on bone marrow mononuclear cells of a patient with acute myeloid leukemia with erythroid differentiation of the blasts and on peripheral blood mononuclear cells of a patient with acute myeloid leukemia with megakaryocytic differentiation of the blasts. The dataset contains raw fastq files of these two samples with single-cell RNA sequencing performed using the 10x Genomics platform.

  Dataset EGAD00001009865

• Detection of early seeding of Richter transformation in chronic lymphocytic leukemia

  Dataset accompanying the study entitled “Detection of early seeding of Richter transformation in chronic lymphocytic leukemia” (Nadeu et al. Nature Medicine 2022), which includes the analysis of longitudinal samples of 19 chronic lymphocytic leukemia patients developing Richter transformation.

  Study EGAS00001006327

• X chromosome dosage and the impact on the methylation pattern across human tissues

  Study EGAS00001007020

• Developmental Dynamics of Translation in the Human Brain

  We performed ribosome profiling and RNA sequencing from a total of 43 adult brain and 30 prenatal brain samples. The age of adult brain donors ranged from 18 to 82 years (average 39.5 years), with an average post-mortem interval of 9.9 hours. The gestational age of prenatal cortex samples ranged from 12 to 23 weeks, with a mean of 19.9 weeks. 

  Study phs002489

• Mapping regulatory variation in sensory neurons using IPS lines from the HIPSCI project

  Sensory neurons are nerve cells that are activated by sensory input such as heat, light and convey information to the brain. Although a key cell type in complex organisms, human sensory neurons are challenging to study because they are impossible to obtain from living donors. We have collaborated with the Neucentis Pharmaceutical Research Unit to differentiate sensory neuron like cells from human induced pluripotent stem cells derived as part of the Human Induced Pluripotent Stem Cells Initiative. We will sequence RNA from 100 IPS lines derived from healthy individuals and perform RNA-seq on the differentiated cells to identify noncoding variants that alter gene expression in human sensory neurons.

  Dataset EGAD00001003145

• Identification of differentially expressed protein-coding genes in HCC and adjacent non-cancerous tissues

  Twenty samples were collected in pairs, i.e., HCC tissue and adjacent non-cancerous tissue. The collected tissue samples were stored in liquid nitrogen. First, 50 mg of tissue was lysed in TRIzol (Invitrogen) to extract RNA following the manufacturer’s instructions. Next, ribosomal RNA was depleted using a RiboZero Gold kit (Epicentre Bio-technologies). RNA integrity was assessed with an Agilent Bioanalyzer 2100. An RNA-Seq library was generated with the rRNA-depleted samples using an Illumina standard RNA Sample Prep kit according to the manufacturer’s instructions. The library was subsequently sequenced on an Illumina HiSeq2500 as 125-bp paired-ends with approximately 300-bp size selection.

  Dataset EGAD00001003397

• T-VEC CBCL scRNA

  We are presenting raw and processed data of our study where we analyze fine-needle aspirate (FNA) samples of primary cutaneous B-cell lymphoma patients undergoing oncolytic virotherapy (https://clinicaltrials.gov/ct2/show/NCT03458117). We are uploading single cell RNA-sequencing and immune repertoire profiling data of 29 FNA samples from four pCBCL patients. The four patients have three different subtypes of primary cutaneous B-cell lymphoma: pCDLBCL-LT, pCFCL and pCMZL. The samples are taken at different time points following T-VEC injection (from baseline up to 91 days after injection). We are uploading the sequences in BAM format and the outputs of the cellranger pipeline (count matrices and filtered VDJ contigs) in CSV format.

  Dataset EGAD00001006829

• The Xq22.3 contiguous gene deletion syndrome (ATS-ID): from genotype to further delineation of the phenotype

  Dac EGAC00001002153

• HCA_Heart_Adult_Wellcome_spatial

  Spatial transcriptome analysis of the human heart

  Study EGAS00001007848

• Tandem DNA Repeats Activate hTERT Gene Transcription

  Multiple independent sequence variants of the hTERT locus have been associated with telomere length and cancer risks in genome-wide association studies. Here, we identified an intronic variable number tandem repeat, VNTR2-1, as an enhancer-like element, which activated hTERT transcription in a cell and chromatin-dependent manner. VNTR2-1, consisting of 42-bp repeats with an array of E-boxes, cooperated with the proximal promoter in hTERT regulation by bHLH transcription factors and maintained hTERT expression during embryonic stem cell differentiation. Genomic deletion of VNTR2-1 in MelJuSo melanoma cells markedly reduced hTERT transcription, leading to telomere shortening, cellular senescence, and impairment of xenograft tumor growth. Interestingly, VNTR2-1 lengths varied widely in human populations.  To assess the genetic polymorphism of VNTR2-1 in human populations, we analyzed genomic DNA samples of Caucasian Americans and African Americans enrolled in the Georgia Centenarian Study.  VNTR2-1 in these genomic DNA samples were PCR amplified and subjected to sequencing analysis usinb the PacBio® SMRT method. The result showed that all VNTR2-1 alleles in Caucasian Americans contained 76 or more 42-bp repeats, whereas 32% of VNTR2-1 alleles in African Americans had fewer than 76 repeats.  

  Study phs002428

• A GWAS study with the AlpeDPD study cohort

  A genome-wide association study (GWAS) with patients treated with fluoropyrimidines was performed to identify genetic variants linked to the severe fluoropyrimidine-related toxicity.

  Study EGAS00001007855

• Human Evolution 3

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released.

  Dataset EGAD00001001373

• BLUEPRINT Epigenetic characterization of megakaryocytes and erythroblasts

  Megakaryocytes and erythroblasts derive from the same progenitor cell type but carry out very different functions. In order to understand how the different functional phenotypes arise we have characterised the epigenetic landscape of these cells.

  Dataset EGAD00001001871

• WGS data from the MESOMICS project (French project of molecular characterization of malignant pleural mesothelioma)

  The dataset includes cram files from WGS of 115 tumor samples as well as 43 matched normal tissue or blood. The sequencing was done with HiSeq X Five instrument.

  Dataset EGAD00001007023

• Orolova hIPSC data access policy

  DAC associated with the hiPSC cell lines generated by the Orlova lab.

  Dac EGAC50000000744

• Hepatocellular carcinoma xenografts established from needle biopsies preserve the characteristics of the originating tumors

  Study EGAS00001003396

• Genomic insight into the origins and dispersal of the Brazilian Coastal Natives

  Study EGAS00001004036

• The Genomic Landscape of Endocrine Resistant Advanced Breast Cancers: Paired Pre- and Post-endocrine Therapy Samples.

  The genomic evolution of breast cancers exposed to systemic therapy and its effects on clinical outcome have not been broadly characterized. We integrated the genomic sequencing of 1918 breast cancers, including 1501 hormone receptor-positive tumors, with detailed clinical information and treatment outcomes. Functional mutations in ERBB2 and loss-of-function mutations in NF1 were more than twice as common in post-endocrine therapy tumors compared to treatment-naive tumors. Additional alterations in the MAPK pathway (EGFR, KRAS among others) and in estrogen receptor transcriptional regulators (MYC, CTCF, FOXA1 and TBX3) were also more common compared to hormonal therapy-naive tumors. To determine whether candidate genomic lesions in the MAPK pathway and estrogen receptor transcriptional regulators were present prior to therapy or whether such lesions arose under the selective pressure of therapy, we performed whole-exome sequencing in select patients who had adequate samples acquired prior to and after progression on endocrine therapy. In total, 95 specimens corresponding to 30 treatment-naive primary tumors, 35 post-treatment tumors, and 30 normal samples were sequenced from 30 patients with endocrine-resistant metastatic breast cancer.

  Study phs001674