16624 results for "sec+and+unspecified+malignant+neoplasm"

in 34.71 milliseconds.

• Analysis of transcriptomic data

  Thirty six samples were sequenced and analysed.

  Dataset EGAD00001008864

• Genetic factors underlying premature coronary heart disease in patients with normal coronary arteries

  The study will analyse by exome sequencing 42 Greek patients with premature MI and no vessel disease to identify genetic factors underlying this condition.

  Dataset EGAD00001000402

• Copy number profiling using PlasmaSeq

  In order to establish copy number profiles from the various samples we prepared libraries and subjected them to whole-genome sequencing at a shallow sequencing depth (0.1x)

  Dataset EGAD00001000761

• WES data

  This is the Whole Exome Sequencing (WES) data from 59 samples from 11 patients with lung adenocarcinomas including 48 tumor samples and 11 peripheral white blood cell samples

  Dataset EGAD00001000984

• Flemish_Gut_Flora_Project_phenotype

  Here, we studied well-phenotyped individuals from the Flemish Gut Flora Project (FGFP, N=1,106, Belgium) and the effect of environments on microbiome. The 69 major significant phenotypes found in this study are provided.

  Dataset EGAD00001001943

• SCNA-Seq of plasma DNA samples

  Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping in plasma DNA of prostate cancer patients

  Dataset EGAD00001002149

• NeurOmics_HD_Biomarker-1_V1

  This data set includes RNAseq data from 136 samples from the TRACK-HD cohort including premanifest, manifest and control subjects. Data can only be used for Huntington's disease related research.

  Dataset EGAD00001002699

• Dataset WES of RRMM patients

  Dataset consists of forty vcf files, outcome of variant calling with caveman algorithm of matched bam file (TUMOR and NORMAL) of RRMM patients. Bam files were obtained from whole exome sequencing!

  Dataset EGAD00001005098

• 10X Genomics WGS data of de novo assembly individual EGYPT

  10x Genomics linked read data used in variant phasing and de novo assembly scaffolding for the EGYPT individual (mapped against GRCh38).

  Dataset EGAD00001006035

• Somatic evolution in the non-neoplastic IBD affected colon

  Whole genome and whole exome sequencing data supporting the manuscript 'Somatic evolution in the non-neoplastic IBD affected colon' by Sigurgeir Olafsson et al.

  Dataset EGAD00001006061

• The University of Hong Kong Intestinal Metaplasia Organoids Study RNASeq Data

  RNASeq data generated from organoid cultures established from normal gastrointestinal organoids, long-term and paired tumor frozen tissues.

  Dataset EGAD00001015421

• Sequencing data for oesophageal and related samples - Ganguli et al (sWGS)

  Data supporting: "TBC" Ganguli et al (sWGS for 75 samples)

  Dataset EGAD00001011189

• Effects of busulfan, fludarabine and clofarabine treatment on human small intestinal organoids.

  Instestinal organoids treated with either busulfan, fludarabine or clofarabine for 24h

  Dataset EGAD00001011336

• Heritable pulmonary arterial hypertension - new genetic findings and environmental triggers

  This dataset contains whole exome sequencing data of 13 family members of 5 heritable pulmonary arterial hypertension families.

  Dataset EGAD50000001817

• WGBS of stepwise-edited melanoma model

  This dataset contains WGBS of a stepwise-edited, human melanoma model including in vitro samples and corresponding xenografts.

  Dataset EGAD50000001317

• HRR gene mutation analysis

  Mutation analysis of cfDNA from urine (stored at various storage conditions) and plasma using the QIAseq HRR panel

  Dataset EGAD50000001586

• Primary human hepatocyte ATAC-seq

  Profiling the chromatin accessibility landscape of cultured primary human hepatocytes (PHH) from three female and three male adult, non-diabetic donors.

  Dataset EGAD50000001751

• RODAM cohort: 16S gut microbiome data

  16S rRNA sequencing data of fecal samples of 1211 RODAM cohort participants in three research sites: rural Ghana, urban Ghana and Amsterdam, the Netherlands.

  Dataset EGAD50000001182

• WGS of primary mediastinal large B-cell lymphoma

  This dataset includes 19 bamfiles of tumor, relapsed tumor and normal samples derived from 7 patients.

  Dataset EGAD50000000494

• Targeted sequencing of genomics regions of interest in depression and obesity

  Data corresponding to the fastq of the 654 individuals included in the study.

  Dataset EGAD50000000476

• WGS data of multiple myeloma

  Dataset containing WGS data from 4 patients with 17 samples with multiple myeloma. The sequencing was always paired and performed using Illumina NovaSeq 6000

  Dataset EGAD50000000437

• Nanopore sequencing of brain tumor tissue obtained by cavitating ultrasonic aspiration

  This dataset contains 21 pediatric brain tumor cases which where obtained during surgery using a cavitating ultrasonic aspiration and submitted to nanopore whole genome sequencing.

  Dataset EGAD50000000269

• SNPArray_TW

  The compressed file contains plink format file for the Affymetrix Human Origins SNP array data of 55 individuals generated and analyzed in Liu et al 2023 study of Taiwanese groups.

  Dataset EGAD00010002424

• MethylationEPIC_850K

  This dataset includes IDAT files from 160 samples (57 primary prostate cancers, 95 proste-derived brain metastases, and 7 normal tissues). The samples were profiled using the Illumina Infinium MethylationEPIC BeadChips (850K)

  Dataset EGAD00010002372

• Microarray_cases

  CASE SAMPLES USING Affymetrix SNP6.0 technology (Thermo Fisher Scientific company): OncoScan FFPE Assay Kit was used for FFPE tissue samples (designed for degraded DNA) and the Cytoscan HD Array Kit was used for the fresh-frozen tissues

  Dataset EGAD00010002034

• GCAT| SNParray coreSpain V2

  4988 samples issued from GCAT cohort, genotyped with MEGAex-Infinium Array, with data for Cr1-22. Plink files with QC and imputed (SHAPEIT+IMPUTE).

  Dataset EGAD00010001664

• Genomic alterations in MM - CEL

  RNA from the same tumor sample (n=98) was also processed using the 3' IVT kit (Affymetrix) and hybridized to U133 Plus 2.0 arrays (Affymetrix).

  Dataset EGAD00010001577

• Surgery in combination with immune checkpoint therapy as an effective treatment for patients with metastatic cancer.

  Abstract Surgical removal of primary tumors was shown to reverse tumor-mediated immune suppression in pre-clinical models with metastatic disease. However, how cytoreductive surgery in the metastatic setting modulates the immune responses in patients, especially in the context of immune checkpoint therapy (ICT)-containing treatments is not understood. Here, we report the first prospective, non-comparative clinical trial (N=104) using three different ICT-containing strategies plus cytoreductive or “debulking” surgery to remove the primary tumor-bearing kidney or a metastatic lesion as a treatment for patients (N=43) with metastatic clear cell renal cell carcinoma (mccRCC). For those patients (N=61) who were not candidates for cytoreductive surgery, a biopsy was obtained instead for correlative biological studies. Our data demonstrated that the combination of ICT with cytoreductive surgery was safe and feasible in patients with mccRCC. The 2-year overall survival was 84% with a median OS of 54.7 months for patients who received ICT containing regimens plus surgery. Immune-monitoring studies with co-detection by indexing (CODEX) identified distinct tumor spatial conformation of cellular subsets as a novel and improved predictor of response to ICT. Importantly, single-cell RNA-sequencing data demonstrated that surgical removal of the tumor increased antigen-presenting dendritic cell population with a concurrent reduction in KDM6B expressing immune-suppressive myeloid cells in the peripheral blood. Together, this study highlighted the feasibility of combining ICT with cytoreductive surgery in a metastatic setting and demonstrated potential enhancement of immune responses following ICT plus cytoreductive surgery in patients with metastatic disease.

  Study EGAS00001005667

• First genome-wide association study in an Australian Aboriginal population provides insights into genetic risk factors for Body Mass Index and Type 2 Diabetes

  A body mass index (BMI) >22kg/m2 is a risk factor for type 2 diabetes (T2D) in Aboriginal Australians. To identify loci associated with BMI and T2D we undertook a genome-wide association study using 1,355,133 quality-controlled single nucleotide polymorphisms (SNPs) genotyped (Illumina 2.5M Duo Beadchip) in 402 individuals in extended pedigrees from a Western Australian Aboriginal community. Imputation using the thousand genomes (1000G) reference panel extended the analysis to 6,724,284 post quality-control autosomal SNPs. No associations achieved genome-wide significance, commonly accepted as P<5x10-8. Nevertheless, genes/pathways in common with other ethnicities were identified despite the arrival of Aboriginal people in Australia >45,000 years ago. The top hit (rs10868204 Pgenotyped=1.50x10-6; rs11140653 Pimputed_1000G=2.90x10-7) for BMI lies 5’ of NTRK2, the type 2 neurotrophic tyrosine kinase receptor for brain-derived neurotrophic factor (BDNF) that regulates energy balance downstream of melanocortin-4 receptor (MC4R). PIK3C2G (rs12816270 Pgenotyped=8.06x10-6; rs10841048 Pimputed_1000G=6.28x10-7) was associated with BMI, but not with T2D as reported elsewhere. BMI also associated with CNTNAP2 (rs6960319 Pgenotyped=4.65x10-5; rs13225016 Pimputed_1000G=6.57x10-5), previously identified as the strongest gene-by-environment interaction for BMI in African-Americans. The top hit (rs11240074 Pgenotyped=5.59x10-6, Pimputed_1000G=5.73x10-6) for T2D lies 5’ of BCL9 that, along with TCFL2, promotes beta-catenin’s transcriptional activity in the WNT signaling pathway. Additional hits occurred in genes affecting pancreatic (KCNJ6, KCNA1) and/or GABA (GABRR1, KCNA1) functions. Notable associations observed for genes previously identified at genome-wide significance in other populations included MC4R (Pgenotyped=4.49x10-4) for BMI and IGF2BP2 Pimputed_1000G=2.55x10-6) for T2D. Our results may provide novel functional leads in understanding disease pathogenesis in this Australian Aboriginal population.

  Study EGAS00001001004

• Genomic Analysis of Primary Plasma Cell Leukemia reveals Complex Structural Alterations and High Risk Mutational Patterns

  Primary plasma cell leukemia (pPCL) is a rare and aggressive form of multiple myeloma (MM) that is characterized by circulating plasma cells. Overall survival remains poor despite advances of anti-MM therapy. In an attempt to identify key biological mechanisms that result in the aggressive pPCL phenotype we performed whole exome sequencing of 23 patients with pPCL. For matched non-tumor control for each patient to exclude germline variants we used CD34+ cells from stem cell harvest (n=20) or cells obtained from buccal swabs (n=3). Tumor samples were from bone marrow derived CD138+ cells. Tumor samples were compared to the germline control to identify somatic abnormalities.

  Study EGAS00001003834

• Identification and functional characterisation of a rare MTTP variant underlying familial non-alcoholic fatty liver disease

  We identified a rare causal variant in MTTP, c.1691T>C p.I564T (rs745447480) encoding microsomal triglyceride transfer protein (MTP) causing progressive non-alcoholic fatty liver disease with cirrhosis and hepatocellular carcinoma unrelated to metabolic syndrome, without manifestations of abetalipoproteinemia, in a four generation family with South Asian ancestry. Variant-expressing hepatocyte-like-cells (HLCs) derived from human induced pluripotent stem cells generated from homozygous donor skin fibroblasts had lower lipoprotein ApoB secretion, compared to wild type cells. Cytoplasmic triglyceride accumulation in HLCs triggered endoplasmic reticulum stress, secretion of pro-inflammatory mediators, production of reactive oxygen species, delineating the progression of disease associated with homozygosity for MTTP p.I564T

  Study EGAS00001005254

• EGA FUSE Client

  EGA FUSE Client What is EGA FUSE Client? The EGA FUSE Client is a Java Native Runtime (JNR) based Filesystem in Userspace (FUSE) client that allows users to access authorised EGA files by presenting them in a virtual directory. This means that users can use authorised EGA files like regular files without having to download them first. The EGA FUSE Client is a useful tool for researchers who need to access and work with large amounts of EGA data. Why use EGA FUSE Client? The EGA FUSE Client provides several benefits for researchers working with EGA data: Efficient use of storage space: With the EGA FUSE Client, users can access authorised EGA files without having to download them first. This means that users can save storage space on their local machines. Faster access to data: Since users can access authorised EGA files directly through the EGA FUSE Client, they can work with the data more quickly than if they had to download the files first. Simplified workflow: The EGA FUSE Client presents authorised EGA files in a virtual directory, allowing users to work with the files like regular files. This simplifies the workflow for researchers who need to access and work with large amounts of EGA data. Get started with EGA FUSE Client To get started with EGA FUSE Client visit the EGA FUSE Client GitHub repository for more information and installation instructions.

  Documentation access/download/visualisation/fuse-client

• The T cell receptor repertoire of tumor infiltrating T cells is predictive and prognostic for cancer survival

  Transcriptomic sequencing on pre-immunotherapy melanoma patients.

  Dataset EGAD00001007710

• AmsterdamUMC Data Access Committee for the EPIC-CD study

  The current data access committee reviews and assesses data requests of researchers that seek to gain access to data acquired as part of the EPIC-CD project as performed at the AmsterdamUMC, Amsterdam, Netherlands.

  Dac EGAC50000000097

• DAC for Liquid CNA in High Grade Serous Ovarian Cancer

  Low pass sequencing of sequential cell free and tumour DNA with matched whole genome sequencing from five patients with high grade serous ovarian cancer presented in Hockings et al Cancer Research paper, 2025.

  Dac EGAC50000000648

• Dynamic human admixture histories over the past ~1,300 years at the northern Himalayan frontier

  Data access for present-day whole-genome dataset (fastq and bam files) from the study titled "Dynamic human admixture histories over the last ~1,300 years at the northern Himalayan frontier"

  Dac EGAC50000000760

• Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population

  We mapped microRNA expression quantitative trait loci by quantifying microRNA expression using small RNA sequencing.

  Study JGAS000504

• Amplicon sequencing of adenoma to carcinoma paired samples from colon

  Colorectal cancer panel sequencing of 100 adenoma and carcinoma samples . Cancer Hot Spot panel sequencing of 7 samples from one poly.

  Dataset EGAD00001004848

• H3Africa H3AChipDesign NEEDI

  50 samples from Mali generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.

  Dataset EGAD00001004334

• Melanoma Germlines subset for BAP1

  These samples comprise both melanoma cases and controls sequenced for a selection of loci linked to disease susceptibility. These bams are a subset of the sequencing restricted specifically to the GRCh37 coding areas of the BAP1 gene.

  Dataset EGAD00001002743

• Dataset for glioblastoma panel sequencing

  This dataset contains panel sequencing data of 228 samples from patients with glioblastoma. Sequencing has been performed on Illumina NovaSeq 6000 and NextSeq 500. The sequencing was always paired.

  Dataset EGAD00001015505

• CBB post-mortem hippocampal short-RNA-seq

  Short RNA sequencing of post-mortem human hippocampi from the Calgary Brain Bank. The dataset includes patients with Alzheimer's disease (AD) and healthy control individuals (Ctrl).

  Dataset EGAD00001006886

• Gene expression associated with Klinefelter syndrome

  RNA-sequencing profiling of leucocytes from peripheral blood samples from 9 KS patients, 9 control males and 13 female controls

  Dataset EGAD00001010078

• DIME

  Shotgun sequencing data from subject as baseline and after 4 weeks of daily doses of low, medium or high CFU Eubacterium hallii L2-7. The strain contained in the drink "Ela" was also sequenced.

  Dataset EGAD00001004849

• whole genome sequencing

  Whole-genome sequencing was performed by Illumina Inc (San Diego, CA). Libraries were constructed with ~300bp insert length and paired-end 100bp reads were sequenced on Illumina HiSeq2000.

  Dataset EGAD00001000782

• Normal brain controls for ICGC PedBrain DNA methylation sequencing

  DNA methylation profiling of 8 control samples from adult (4) and fetal brain (4)

  Dataset EGAD00001000952

• Paired-end sequenced plasma DNA samples

  Merged file of low-coverage WGS from 179 plasma DNA samples from non-cancer controls and cancer patients for assessment of size distribution of plasma nuclear DNA fragments.

  Dataset EGAD00001002217

• Single-cell RNA sequencing

  Single-cell RNA sequencing on 10 antrum and 4 body gastric biopsies

  Dataset EGAD00001010166

• WXS files for AML data

  WXS files for paper titled "Integrative Analysis of Pediatric Acute Leukemia Identifies Acute Myeloid/T-Lymphoblastic Leukemia Subtype that Spans a T Lineage and Myeloid Continuum with Distinct Prognoses"

  Dataset EGAD00001006443

• RNASeq files for AML data

  RNASeq files for paper titled "Integrative Analysis of Pediatric Acute Leukemia Identifies Acute Myeloid/T-Lymphoblastic Leukemia Subtype that Spans a T Lineage and Myeloid Continuum with Distinct Prognoses"

  Dataset EGAD00001006444

• Acquired RAD51C promoter methylation loss causes PARP inhibitor resistance in high grade serous ovarian carcinoma

  Analysis of RAD51C promoter methylation using targeted bisulfite sequencing (amplicon sequencing) in ovarian cancer pre-clinical models and patient samples.

  Dataset EGAD00001007799

• WGS files for AML data

  WGS files for paper titled "Integrative Analysis of Pediatric Acute Leukemia Identifies Acute Myeloid/T-Lymphoblastic Leukemia Subtype that Spans a T Lineage and Myeloid Continuum with Distinct Prognoses"

  Dataset EGAD00001006442

• Somatic mutations called from whole-exome sequencing of PSCCE

  We performed whole-exome sequencing on 46 pairs of PSCCE and matched normal sample. Somatic mutations were called using MuTect2.

  Dataset EGAD00001006743

• ChIPseq data for Glioblastoma (EGAS00001003953, H016)

  ChIPseq data for human glioblastoma patients, EGAS00001003953. Mix of input, H3K27ac, H3K27me1, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me3 and BRD, 20 human samples, 2 cell lines (LN229, ZH487).

  Dataset EGAD00001006548

• Adenoid Cystic Carcinoma

  Whole genome sequencing data for 25 adenoid cystic carcinoma samples. The samples were used for Illumina TruSeq library construction and were sequenced on an Illumina HiSeq 2000. The PE fastq files are provided.

  Dataset EGAD00001003959

• non-IVF MeDIP-seq bam files

  Bam files consisting of aligned MeDIP-seq reads from cord blood cells and cord blood mononuclear cells of twins not conceived through in vitro fertilisation

  Dataset EGAD00001003159

• WES data from 5 DGCR8 schwannomas

  This dataset contains the exome sequencing data (BAMs, VCFs and CNVs) from 5 schwannoma tumors from the same patient.

  Dataset EGAD00001008200

• CBD-KEY-SUMMARIES: Other data

  Other raw and processed phenotype data generated by the COMBAT consortium.

  Dataset EGAD00001008009

• STAR outputs from RNA-seq

  STAR outputs from RNA-seq of 84 pancreatic neuroendocrine neoplasms, 10 normal islet samples and 4 cell line samples.

  Dataset EGAD00001006991

• multi regional whole exome sequencing of gastric adenocarcinoma

  Multiregional whole-exome sequencing was done using 48 tumor samples (range: 4-10 tumor samples/patient) from 9 patients with adenocarcinomas of the stomach and gastroesophageal junction (GC)

  Dataset EGAD00001006251

• H3Africa H3AChipDesign CAfGEN

  48 samples from Botswana generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.

  Dataset EGAD00001004533

• Recurrent somatic JAK-STAT mutations within a RUNX1-mutated pedigree

  Whole-exome sequencing of a RUNX1-mutated pedigree, including samples from mother, father and four offsprings. Recurrent somatic JAK-STAT mutations were found among the diseased individuals.

  Dataset EGAD00001002240

• The Extracellular RNA Quality Control (exRNAQC) study (phase 1)

  mRNA capture sequencing and small RNA sequencing data (FASTQ files) of the exRNAQC study phase 1.

  Dataset EGAD00001007697

• 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

• Single-cell RNA sequencing of CML patients

  This dataset contains 15 single-cell RNA sequencing samples from 6 CML patients before and after TKI-cessation. The raw data is available as fastq files.

  Dataset EGAD00001012842

• RNA-sequencing of adult T-cell leukemia/lymphoma sample

  This dataset includes 10 RNA-sequencing (RNA-seq) data for 9 primary tumors and 1 cell line from adult T-cell leukemia/lymphoma (ATL).

  Dataset EGAD00001004937

• ctDNA data

  ctDNA data for IMpower150, including individual mutation calls (one mutation per sample per line), sample list including ctDNA status (one sample per line), and patient-level ctDNA summaries called ctDNA features (one patient per line).

  Dataset EGAD00001009725

• Illumina RNA sequencing data

  RNA sequence data for HKCI-2, HKCI-C1, HKCI-C2, HKCI-C3 and MIHA. RNA-seq data of all the 5 samples were stored in compressed fastq format.

  Dataset EGAD00001004476

• Dataset for HCPlus_WES

  WES/WGS sequencing data of 234 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009272

• GCAT| WGS VCF Raw Genotypes V1

  This dataset contains raw genotypes ( SNVs, Indels and SVs), from 785 samples,without applying any filter, from the 808 WGS GCAT cohort.

  Dataset EGAD00001008210

• PrevANZ RNAseq dataset

  Whole blood samples collected at baseline and week 12 in PAXgene Blood RNA tubes. RNA sequencing on the Illumina NovaSeq 6000 System generated 150 base pair length paired end reads.

  Dataset EGAD00001011069

• H3Africa H3AChipDesign ELSI

  24 samples from Cameroon generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.

  Dataset EGAD00001004316

• H3Africa H3AChipDesign ACCME

  49 samples from Nigeria generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.

  Dataset EGAD00001004505

• Long cell-free DNA molecules in maternal plasma (dataset1)

  Bam files consists PET cases and healthy cases

  Dataset EGAD00001008721

• MGA-NUTM1 fusion in high grade spindle cell sarcoma Data

  There is a total of 4 sample data (2 WGS and 2 RNAseq) belong to 2 patient deposited in this study.

  Dataset EGAD00001004479

• Smart-seq2 single-cell RNA-seq of human liver non-parenchymal cells

  Smart-seq2 single-cell RNA-seq of human liver non-parenchymal cells from lean and obese individuals

  Dataset EGAD00001010301

• Exome reads

  One sample of human genomic DNA. DNA extracted from whole blood. Reads obtained using an exome enrichment kit (Truseq, Illumina) and sequencing of 100bp paired-end reads on a HiSeq 2500 sequencing system (Illumina).

  Dataset EGAD00001003841

• H3Africa H3AChipDesign TrypanoGEN2

  41 samples from Zambia generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.

  Dataset EGAD00001004220

• H3Africa H3AChipDesign TrypanoGEN1

  26 samples from Cameroon generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.

  Dataset EGAD00001004393

• RNA sequencing of undifferentiated sarcomas

  mRNA sequencing of 50 undifferentiated sarcoma tumour samples and 5 adjacent muscle tissue samples. BAM files are provided, with metadata specifying which samples are tumour/normal.

  Dataset EGAD00001004439

• Whole exome sequencing for ZNF384-rearranged ALL cases

  Whole exome sequencing for the matched germline and tumor DNA from 10 ALL cases with ZNF384 rearrangements.

  Dataset EGAD00001002152

• Southern African Human Genome Programme dataset

  The SAHGP characterises the genomes of 24 individuals (8 Coloured and 16 black southeastern Bantu-speakers) using deep whole genome sequencing (WGS).

  Dataset EGAD00001003791

• Breast RNA Sequencing

  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 EGAD00001001340

• BASIS RNA Sequencing

  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 EGAD00001001341

• Single Cell Targeted Sequence Capture

  This study is to ascertain whether it is feasible to extract single cell from a tumour, perform amplification, generate a library and sequence a targeted pulldown.

  Dataset EGAD00001001450

• EBV-AID project

  Whole genome sequencing of EBV-transformed B cells in order to determine whether EBV induction of activation-induced cytidine deaminase (AID) produces genome-wide mutations and/or chromosomal rearrangements.

  Dataset EGAD00001001458

• Targeted sequencing of patients with neurodegenerative diseases

  A targeted gene panel that covers coding, noncoding, and short tandem repeat regions improves the diagnosis of patients with neurodegenerative diseases

  Dataset EGAD00001005114

• WES data for Family 2 from optic atrophy study

  The dataset includes the BAM files from WES experiments performed on a proband presenting with syndromic optic atrophy and his healthy parents - Family 2 in our study

  Dataset EGAD00001005344

• KIT-dependent and -independent genomic heterogeneity of resistance in gastrointestinal stromal tumors - TORC1/2 inhibition as salvage strategy

  The mutational status of GIST analyzed with a broad sequencing approach (WES, RNAseq)

  Study EGAS00001003405

• RNA-Seq of serially passaged TIC-enriched spheres of colorectal cancer

  18 samples of RNA-Seq of serially passaged TIC-enriched spheres of colorectal cancer (CRC), sequenced on HiSeq2000 and HiSeq2500

  Dataset EGAD00001006264

• RNA-SEQ for the Caldas Lab breast cancer PDTX collection

  RNA-SEQ for the Caldas Lab breast cancer PDTX collection. This includes both single and paired end runs

  Dataset EGAD00001006307

• Fecal whole metagenomic shotgun sequencing data.

  Human fecal WMS data from patients treated with combined anti-CTLA-4 and anti-PD-1 immunotherapy for advanced melanoma.

  Dataset EGAD00001006734

• The University of Hong Kong Intestinal Metaplasia Organoids Study WES Data

  Whole exome sequencing data generated from organoid cultures established from normal gastrointestinal organoids, long-term, spheroid and blood leukocyte DNA.

  Dataset EGAD00001015420

• Transcriptome Profiling of human AT2 cells in COPD

  RNA-seq of FACS sorted AT2 cells from ex-smokers with (n=6) and without (n=3) COPD at different disease stages. Fastq files are provided.

  Dataset EGAD00001011115

• Methylation Profiling of human AT2 cells in COPD

  WGBS of FACS sorted AT2 cells from ex-smokers with (n=6) and without (n=3) COPD at different disease stages. Fastq files are provided.

  Dataset EGAD00001011116

• Clinical Utility of BRCA Research by Inocras, CMC and SMC (CUBRICS)

  This dataset consists of whole-genome sequences from 1,364 Korean breast cancers

  Dataset EGAD50000001994

• Dataset of single cell RNA sequencing of peripheral blood HSPC

  Here, we conducted peripheral blood CD34+ cells single-cell RNA sequencing of patients with sickle cell anemia (n=4) and healthy donors (n=3)

  Dataset EGAD50000001522

• Bulk transcriptomics of Human High-Grade-B-Cell-Lymphomas differentiated according to IGH status

  GCB DLBCL MB2 DE and HGBCL-DH-BCL2(-BCL6) cases classified according to IGH status in IGH+ or IGH-undetectable

  Dataset EGAD50000001524

• Single-cell RNA-seq from tumor-on-chip (TOC)

  8 Fastq files of single-cell RNAseq data from tumor-on-chip (TOC) after 42h of TNBC and CAF mono- or co-culture

  Dataset EGAD50000001296

• ST lobular manuscript dataset

  Spatial transcriptomics analysis for 43 breast cancer lobular samples. Note that there are 2 runs per sample Images and read counts will be made availalble on Zenodo upon publication.

  Dataset EGAD50000001467