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• Nascent transcriptome in T-ALL bone marrow

  Nascent RNA expression profiles were generated with Global Run-On sequencing (GRO-seq) from T-ALL patient samples to measure primary transcription genome-wide and to summarize the transcriptional activity at gene loci and enhancers.

  Study EGAS00001005864

• Discovery of cancer prognostic markers based on comparison of gene expression in colorectal cancer samples.

  Here, we analyse bulk mRNA-seq data derived from normal tissues adjacent to tumors (NATs) and tumour tissues of colorectal cancer (CRC), including 80 NAT samples and 80 tumour samples.

  Study EGAS00001005068

• Single cell atlas of human glioma

  We profiled 87 primary-recurrentpatient-matched paired GBM specimens with single-nucleus RNA and bulk-DNA sequencing and single-cell open-chromatin and spatial transcriptomics/proteomics assays. We found that recurrent GBMs are characterized by a shift to a mesenchymal phenotype in response to therapy

  Dataset EGAD00001008811

• Genomic and transcriptomic profiling of carcinogenesis in patients with familial adenomatous polyposis

  Whole-exome sequencing (WES) and whole-genome sequencing (WGS) were performed on matched adjacent normal tissues, multiregionally sampled adenomas at different stages and carcinomas from 5 patients with FAP and 1 patient with MUTYH-associated polyposis (MAP) (n=56 exomes; n=56 genomes; n=8,757 single cells).

  Dataset EGAD00001005457

• Characterization of four subtypes in morphologically normal tissue excised proximal and distal to breast cancer

  RNA sequencing data from breast cancers (n=18) and their matched HN tissues (n=36), healthy breast from cosmetic reduction mammoplasty (RM; n=5), and risk reducing mastectomies (RR, n=5), with peritumoral samples excised proximal to (TP, less than 2 cm) and distal from (TD, 5-10 cm) the primary tumor.

  Dataset EGAD00001006291

• Targeted amplicon sequencing on 218 samples from Stage 1 epithelial ovarian cancer biopises

  BAM files (aligned against the hg38 genome) from a targeted amplicon sequencing (139 genes) experiment (median depth 1000X) on 218 samples from Stage 1 epithelial ovarian cancer biopises. Samples labeled "bis" or "tris" with the same ID are relapses; "left" or "right" samples indicate, in the case of bilateral tumor, from which ovary the sample was taken.

  Dataset EGAD00001006873

• 25 metastatic cutaneous squamous cell carcinoma WGS VCF

  whole genome sequencing on lymph node metastases and blood DNA from 25 cSCC patients with regional metastases of the head and neck. We designed a multifaceted computational analysis at the whole genome level to provide a more comprehensive perspective of the genomic landscape of metastatic cSCC. This study contains the majority of 15 samples which are previously submitted in EGAC00001001100.

  Dataset EGAD00001009004

• WXS Tumor Samples Javelin head and neck 100

  We performed Whole Exome (WXS) and RNASeq sequencing on samples obtained from the phase 3 randomized, double-blinded, placebo-controlled study in patients with locally advanced squamous cell carcinoma of the head and neck JAVELIN Head and Neck 100 (NCT02952586). There are 471 WXS Tumor samples and 346 RNASeq tumor samples. All tumor samples have matching normal samples.

  Dataset EGAD00001011680

• Javelin head and neck 100

  We performed Whole Exome (WXS) and RNASeq sequencing on samples obtained from the phase 3 randomized, double-blinded, placebo-controlled study in patients with locally advanced squamous cell carcinoma of the head and neck JAVELIN Head and Neck 100 (NCT02952586). There are 471 WXS Tumor samples and 346 RNASeq tumor samples. All tumor samples have matching normal samples.

  Dataset EGAD00001011290

• Long read mRNA sequencing of blood cells exposed to different immune stimuli

  Long-read (PacBio) RNA sequencing dataset of in vitro stimulated PBMC cells. 5 samples consisting of 1 RPMI control and 4 stimulus conditions (lipopolysaccharide (LPS), polyI-polyC, S. aureus and C. albicans) all originating from one donor. Files are raw BAM format files generated by Sequel 2 machine.

  Dataset EGAD00001009998

• Evaluation of triple negative breast cancer with heterogeneous immune infiltration

  This dataset contains the raw RNA-seq data (FASTQ files) of the samples used in the study title: "Evaluation of triple negative breast cancer with heterogeneous immune infiltration". The dataset is composed of 3 patients with 6 samples per patient (3 with high TILs and 3 with low TILs).

  Dataset EGAD00001010280

• Whole genome sequencing and whole exome sequencing of DIPG tumors and matched normal tissue

  Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling.

  Dataset EGAD00001003305

• TGL49 LFS CHARM panel

  Targeted panel sequencing of hereditary cancer syndrome-associated genes (TP53, BRCA1, BRCA2, PALB2, MLH1, MSH2, MSH6, PMS2, EPCAM, and APC) in plasma and buffy coat samples from patients with Li-Fraumeni syndrome.

  Dataset EGAD00001010011

• Exome sequencing of two siblings with a neurodegenerative disorder identifies causative compound heterozygous variants in SLC5A6

  Exome sequencing data of two siblings of with a neurodegenerative phenotype due to SMVT deficiency. Exonic sequences were enriched using the SeqCap EZ Human Exome Library v3.0 kit (Roche NimbleGen) and libraries sequenced as 100bp paired-end reads on the HiSeq 2000 platform (Illumina).

  Dataset EGAD00001005364

• Genomic Analysis of Anaplastic Thyroid Carcinoma

  This dataset includes WGS & WTS alignment data generated from 1 ATC tumor, its matched peripheral blood specimen and 3 authenticated ATC cell lines, THJ-16T, THJ-21T and THJ-29T. In addition, it includes WTS data from extra 4 unique anaplastic cell lines, ACT-1, C643, HTh7 and T238.

  Dataset EGAD00001001321

• Exome sequencing data from tumor progression cohort

  This dataset, named Stockholm tumor progression cohort, contains exome-sequencing samples of matched primary and metastasis samples from 20 metastatic breast cancer patients. All patients have one or more sequenced normal samples as well. The total number of samples is 125. The dataset has been used, apart from other studies, to explore tumor evolution patterns in metastatic breast cancer at Karolinska Institute Stockholm.

  Dataset EGAD00001003837

• Mechanism of action and resistance to Trastuzumab Deruxtecan in patients with metastatic breast cancer: the DAISY trial

  195 exome sequencing samples

  Dataset EGAD00001011110

• Whole Exome sequencing of Gingivo-buccal Cancer - ICGC India Project Batch04

  This dataset pertains to whole exome sequencing of paired DNA samples of Gingivo-buccal oral cancer patient.DNA was isolated from the tumor and blood tissues of 47 patients (94 samples).We have performed Nextera exome capture and sequenced exome libraries in Illumina HiSeq platform.We have uploaded BWA-ALN aligned BAM files.

  Dataset EGAD00001003987

• Complete Metagenomics from feces

  Complete Microbiome Metagenomics from feces of 461 IBD patients; The sequencer used was the Illumina HiSeq 2000 with a paired end reads design, reflected in the 2 FastQ format files per sample.

  Dataset EGAD00001004194

• PIK3R4 (VPS15)

  WES of human: A mutation in VPS15 (PIK3R4) causes a ciliopathy and affects IFT20 release from the cis-Golgi WES (Agilent SureSelect All Exon XT2 50 Mb kit) has been realized on three affected siblings (II.1, II.3, II.5) and one healthy sister (II.4). Raw data (BAM files) are provided: - II.1.aligned.sorted.dedup.realign.recal.bam - II.3.aligned.sorted.dedup.realign.recal.bam - II.5.aligned.sorted.dedup.realign.recal.bam - II.4.aligned.sorted.dedup.realign.recal.bam

  Dataset EGAD00001002736

• Myeloid gene panel or whole exome sequencing data on blood and bone marrow of 15 individuals with germline RUNX1 mutations to characterize additional somatic mutations.

  This dataset consists of 20 fastq files in total from exome and myeloid gene panel sequencing of 15 carriers of germline RUNX1 mutations from 10 different families.

  Dataset EGAD00001006010

• RNA-seq data of breast cancer HCI011 model from Ros et al (2020)

  RNA-seq data of the HCI011 and HCI011R models, GDC032 treated and control (total of 21 samples), from the paper: FOXM1 is a biomarker of resistance to PI3Kα inhibition in ER+ breast cancer that is detectable using metabolic imaging (Ros et al, 2020)

  Dataset EGAD00001006245

• RNA-seq from PDAC samples

  Bam and fastq files from RNA-seq of PDAC samples used in the PCSI mismatch repair study

  Dataset EGAD00001006261

• Validated Single-cell RNA sequencing in early breast cancer

  Single-cell RNA and VDJ sequencing of early breast cancer

  Dataset EGAD00001006608

• Single-cell TCR sequencing of gluten-specific T cells from 20 celiac disease patients uploaded on 2021_Data access committee

  In order to characterize the T cell receptor (TCR) repertoire of gluten specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.5:DQ2.5-gluten tetramer binding CD4+ T cells isolated from blood, biopsies and T cell line from celiac disease patients.

  Dataset EGAD00001006977