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• Pancreatic Cancer NGS WGS data

  Whole genome sequencing data for Pancreatic Cancer Samples exploring the tandem duplicator phenotype

  Study EGAS50000001078

• MD Anderson OPMD DAC

  Datasets and agreement used for the OPMD dataset access of the publication Reconstructing oral cavity tumor evolution through brush biopsy, Springer Nature, DOI: 10.1038/s41598-024-72946-3

  Dac EGAC50000000384

• V4_Colorectal_panel_test

  Targeted gene screen of cell line tumours for testing the new V4 Colorectal gene panel.

  Study EGAS00001001807

• He et al. WGS data

  This dataset are the bam files of WGS data from the paper by He et al.

  Dataset EGAD00001007133

• Covacta RNAseq merged EGA metadata

  Sample metadata for the RNA-seq dataset. This dataset includes subject-level data and longitudinal visit day information for the corresponding samples.

  Dataset EGAD00001011162

• NSCCG CRC WES

  1006 Familial early onset gemrline CRC patients sequenced by the Molecular and Population Genetics group of the Institute of Cancer Research

  Dataset EGAD00001002204

• GR@ACE_StageI.CEL_files

  Intensity calculation on the pixel values of the DAT file for 7409 samples genotyped using Axiom 815K Spanish Biobank array (Thermo Fisher)

  Dataset EGAD00010001655

• The ERASMUSMC-HEMA Data Access Committee controlling appeals for 3q26-rearranged acute myeloid leukemia datasets from the department of Hematology at Erasmus MC

  Dac EGAC00001000162

• BROCA cancer panel sequencing for 15 samples

  BROCA panel sequencing using the BROCA-HR v8 and BROCA-GO v1 versions of the gene panel

  Dataset EGAD50000000035

• RNA-sequencing from duodenal bipsies of Celiac disease patients

  Total RNA was extracted from the PaxFPE biopsy specimens (n = 116)

  Study EGAS50000000337

• H3Africa KDRN Phenotype

  The phenotypic data for 6431 samples of the KDRN Study from Ghana and Nigeria.

  Dataset EGAD00001009333

• 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

• COMPASS Next Generation Sequencing WGS data

  Whole genome sequencing data for Pancreatic Cancer Samples from the COMPASS clinical trial

  Study EGAS50000001091

• Genomic profiling of two pathogenic germline truncating variants of BRCA2 confer different haploinsufficiency phenotype

  Observation of the loss of heterozygosity of BRCA2

  Study EGAS50000000613

• Haemoglobin_E_beta_thalassaemia_in_a_patient_group_from_Sri_Lanka

  Exome sequencing of 32 patient samples from Sri Lanka with the condition haemoglobin E beta thalassaemia

  Study EGAS00001000626

• Molecular landscape of C1498 cells

  We characterized the genomic background of C1498 cells by whole genome sequencing analysis.

  Study EGAS50000001284

• methylation_bc_cervix

  Raw methylation data from cervical samples in individuals with breast cancer.

  Dataset EGAD00010002081

• BIOMIROX

  This dataset regroups RNAseq of paired primary colorectal cancers and liver metastases extracted from 113 patients In Paris and Besançon University Hospitals. 216 FASTQ files from single-end 3' PolyA (QuantSeq 3′mRNA-Seq Kit FWD for Illumina (Lexogen)) RNAseq samples were generated On NOVASEQ 6000 (ILLUMINA).

  Dataset EGAD50000000443

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96213A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 522 samples; filetype=bam

  Dataset EGAD00001004771

• Single-cell transcriptome of human fetal pancreas and in vitro pancreatic spheroids

  This dataset combines single cell transcriptome data from fetal pancreas at 7-10 wpc, embryonic stem cell-derived pancreas progenitors and spheroids generated from both fetal pancreas and human pluripotent stem cell-derived pancreas progenitors.

  Dataset EGAD00001007506

• Dataset-linking-WGS-via-README-for-EGAS00001004884

  This dataset contains 139 Tumor and Control WGS files for samples for Gerhauser et al.,Cancer Cell, 2018, 34:996-1011. WGS and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001007669

• Alternative splicing in Shh-MB

  We analyzed alternative splicing with Shh medulloblastoma. This dataset contains bam files of whole genome sequencing from 4 cases. Genomic DNA was isolated from both tumor and matched control specimens. We performed whole genome sequence on Illumina Hiseq.

  Dataset EGAD00001004347

• Whole exome sequencing of patient derived cell lines

  Whole exome sequencing of 3 patients derived cell lines and patient blood (N = 6 samples), performed using Agillent SureSelect All Exon V5 and Illumina HiSeq 4000. Data is in raw fastq format (N = 10 fastq pairs, 20 files total), as some samples were split between two lanes.

  Dataset EGAD00001007738

• ChIP-seq ERa and H3K27ac in endometrial healthy and tumor tissues

  ChIP-seq has been perfomed on 4 healthy and 5 tumor fresh-frozen endometrial tissues from post-menopausal patients. Immunoprecipitation has been performed for H3K27ac and ERa. Raw single-end fastq data have been aligned using bwa-mem using Hg19 genome assebly as reference. Aligment bam files are provided.

  Dataset EGAD00001010896

• 300BCG trained immunity scRNAseq

  We have paired 39 individuals in 4 conditions: T0_RPMI (baseline, before BCG and without LPS); T0_LPS (before BCG and with LPS); T3m_RPMI (3 months after BCG, without LPS); T3m_LPS (3 months after BCG, with LPS).

  Dataset EGAD00001010055

• PhIP-Seq Serum 1000IBD

  PhIP-Seq experiment conducted in Eran Sigal's group at WIS.

  Dataset EGAD00001010118

• Whole genome sequencing of HSPC and SI clones of disomy- and trisomy 21 fetuses samples (HiSeq X Ten samples)

  Whole genome sequencing of HSPC and SI clones of 2 disomy- and 1 trisomy 21 fetuses samples (HiSeq X Ten samples). 5 disomy clones and 5 trisomy clones were included in this experiment. Three bulk samples were also included.

  Dataset EGAD00001005459

• Whole genome sequencing data of paediatric T cell acute lymphoblastic leukemia (T-ALL)

  T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy accounting for approximately 15–25% of pediatric and adult ALL cases. Despite significant therapeutic improvements over the last decade, the prognosis of T-ALL remains less favorable than that of B-ALL, with 5-year EFS and OS of around 76–82% and 80–88%, respectively, depending on the treatment protocol used. T-ALL patients often suffer from failure of induction therapy or early relapse, which is associated with a dismal prognosis. Approximately 10–15% of T-ALL patients experience relapse, and survival after relapse is poor.

  Study EGAS50000001387

• InterPregGen-GWAS-KAZ-1

  Preeclampsia (PE) is a syndrome affecting pregnant mothers and fetus/babies characterised by hypertension and proteinuria, and is a leading cause of maternal and fetal death and of premature births worldwide. The InterPregGen Consortium was funded by a European Framework 7 (FP7) grant and grew out of the WTCCC3 GWAS comparing ~2000 UK PE mothers with ~6000 common UK controls. This dataset includes lllumina 2.5-8 genotyping of maternal and fetal PE cases and controls from Kazakhstan. This study is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator).

  Dataset EGAD00010001945

• InterPregGen-GWAS-KAZ-2

  Preeclampsia (PE) is a syndrome affecting pregnant mothers and fetus/babies characterised by hypertension and proteinuria, and is a leading cause of maternal and fetal death and of premature births worldwide. The InterPregGen Consortium was funded by a European Framework 7 (FP7) grant and grew out of the WTCCC3 GWAS comparing ~2000 UK PE mothers with ~6000 common UK controls. This dataset includes OmniExpress genotyping of maternal and fetal PE cases and controls from Kazakhstan. This study is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator).

  Dataset EGAD00010001947

• InterPregGen-GWAS-KAZ-3

  Preeclampsia (PE) is a syndrome affecting pregnant mothers and fetus/babies characterised by hypertension and proteinuria, and is a leading cause of maternal and fetal death and of premature births worldwide. The InterPregGen Consortium was funded by a European Framework 7 (FP7) grant and grew out of the WTCCC3 GWAS comparing ~2000 UK PE mothers with ~6000 common UK controls. This dataset includes Infinium GSA genotyping of maternal, paternal and fetal PE cases and controls from Kazakhstan. This study is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator).

  Dataset EGAD00010001949

• Targeted pancancer RNA-Seq

  This dataset contains targeted RNA-Seq generated with the Illumina RNA Pan-Cancer panel. It comprises 2200 cancers from children and adults. The cancers represent a wide range of CNS, solid and haematopoeitic tumours. Samples are from pathology specimens including FFPE, fresh frozen, bone marrow aspirate and peripheral blood.The data is used for tumour driver identification. SNVs, indels and fusion detection.

  Study EGAS50000000700

• Population_sequencing_phasing

  Whole-genome sequencing of human individuals from Polynesian and Native American populations, as well as 10x Genomics Chromium data from Polynesian, Native American and Aboriginal Australian populations, allowing for experimental phasing of haplotypes. 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/

  Study EGAS00001001852

• Gene_Characterization_in_Carbohydrate_metabolic_alterations__neonatel_diabetes___congenital_hyperinsulinemic__in_early_childhood

  Whole Exome Sequencing of trios (proband + parents) or probands only with Neonatal Diabetes Mellitus (NDM) or Congenital Hyperinsulinism of Infancy (CHI) of unknown genetic origin. 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 (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002074

• Single-cell RNA-seq of human kidney tumors

  Fresh nephrectomy samples were collected from a total of 5 untreated ccRCC patients. Out of these 5 patients, 7 samples were obtained. Two samples consisted of fresh versus frozen single cells from the primary tumor site of one patient. Two other samples consisted of matched primary and distant thrombus sites (the vena cava) of a second patient. The three remaining samples came from the primary tumor sites of three distinct ccRCC patients. Single-cells were captured into 10x barcoded gel beads and RNA-sequencing library preparation was done using Chromium Single Cell 3' v2 chemistry. Sequencing was performed on a Illumina HiSeq 4000 sequencer.

  Dataset EGAD00001009306

• tRCC UTSW 2024 Cohort

  This submission contains the WES and RNA-Seq raw data for the study titled 'Comparative Genomics of a Translocation Renal Cell Carcinoma Mouse Model Reveals Molecular Mechanisms of Tumorigenesis.

  Dac EGAC50000000105

• Whole Genome Sequencing of Insulinomas

  Whole Genome Sequencing of Insulinomas and paired blood controls from the same patients.

  Study EGAS50000000321

• Tumor Profiler AML Study

  Multi-omics data generated from 22 samples from the Tumor Profiler AML cohort

  Study EGAS50000000577

• V2_Colorectal_panel_test

  Targeted gene screen of cell line tumour samples for testing the new V2 Colorectal gene panel.

  Study EGAS00001001806

• Melanoma post mortem analysis

  We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient.

  Dataset EGAD00001005072

• Single Nuclei RNA sequencing batch 1

  This dataset includes the first 9 PTC samples and 6 ATC samples profiled on the same sequencing flowcell.

  Dataset EGAD00001011366

• Genome-wide characterization of Kuwaiti Arab Population

  All the 620 individuals were genotyped using Illumina HumanOmniExpress arrays for 730,525 SNPs.

  Study EGAS00001005034

• Transcriptome profiling of slice cultures of human embryonic forebrain

  7 samples from slice cultures kept for 4-29 days from forebrain of the developing human embryo at ages between post conceptional week 7.5 and 10.5 were dissociated and single cells were collected and processed without bias for mRNA-seq using the 10Xgenomics chromium 3' protocol version 3. Libraries were sequenced on Illumina NovaSeq 6000 and reads aligned against the human GRCh38 genome.

  Dataset EGAD50000001690

• 10x Visium Spatial Transcriptomics of 61 Human Hepatocellular Carcinoma Samples

  This dataset contains spatial transcriptomics sequencing data from 61 hepatocellular carcinoma (HCC) tissue samples profiled using the 10x Genomics Visium platform. The cohort includes 38 resected tumors and 23 tumors from patients treated with atezolizumab plus bevacizumab. Sequencing data are provided as paired-end FASTQ files. These data support the analysis of intra-tumoral heterogeneity and its association with clinical outcomes.

  Dataset EGAD50000002122

• Genome sequence data from a metastatic squamous cell carcinoma of the oropharynx patient

  Genome sequence data from a metastatic squamous cell carcinoma of the oropharynx patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003691

• Genome and transcriptome sequence data from a metastatic mmmt of the endometrium patient

  Genome and transcriptome sequence data from a metastatic mmmt of the endometrium patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004618

• Genome and transcriptome sequence data from an adenocarcinoma of the lung patient

  Genome and transcriptome sequence data from an adenocarcinoma of the lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003657

• Genome and transcriptome sequence data from an adenocarcinoma of the lung patient

  Genome and transcriptome sequence data from an adenocarcinoma of the lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003742

• Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003076

• Genome and transcriptome sequence data from an adenocarcimona of the lung patient

  Genome and transcriptome sequence data from an adenocarcimona of the lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003616