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• RNAseq data from 112 samples of benign or malignant ovarian tumours

  This dataset contains ~1.2 TB RNA sequencing data in fastq format from 112 samples of fresh-frozen ovarian tumours from a total of 111 women, two samples being replicates. The samples were collected from the U-CAN collection at Uppsala Biobank and include both benign (n = 18) and malignant (n = 94) tumours. The RNA sequencing samples were sequenced using paired-end sequencing (2x150 bp) on an Illumina NovaSeq 6000 instrument at the SciLifeLab National Genomics Infrastructure (NGI) in Uppsala.

  Dataset EGAD50000001521

• RNA, ATAC, ChIP datasets from iPSC Derived Macrophages with and without TNFRSF1A intronic deletion using CRISPR

  This dataset consists of functional genomic data from iPSC derived Macrophages with or without CRISPR deletions and controls. It contains 21 paired end fastq files consisting of 6 total RNA-seq samples and 9 ATAC samples, for ChIP there are 2 H3K4me3 samples, 2 H3K27ac samples along with 2 paired input samples. The samples were sequenced on the Illumina HiSeq4000 amd Illumina NextSeq500 platforms.

  Dataset EGAD50000000984

• Whole-genome and single-cell sequencing of lethal metastatic castration resistant prostate cancer

  Contains a total of 9 patients with whole-genome sequencing of 30 tumours or germline samples, 10X single-cell multiome RNA-seq + ATAC-seq of 24 tumours, 10X 5' single-cell RNA-seq of 10 tumours, and snPATHO-seq of 2 primary tumours. All single-cell experiments have matched whole-genome sequencing. When matched tumour (and germline) whole-genome sequencing is missing, it can be found under EGAS00001006598.

  Dataset EGAD50000001869

• RNA-seq data for proximal and distal human LHBT UZH (CH)

  This dataset contains bulk RNA-seq data from 15 patients who underwent rotator cuff repair surgery, yielding paired proximal and distal samples of the long head of the biceps tendon (30 samples total). The submission includes 90 files, consisting of R1 and R2 FASTQ files for each sample as well asprocessed .TXT files containing gene-level counts generated after genome alignment. Raw sequencing reads were generated on an Illumina platform, aligned to the human reference genome GRCh38.p13, and quantified at the gene level.

  Dataset EGAD50000002095

• RNA sequencing of BCP-LBL and EM B-ALL patients samples

  In order to perform comprehensive transcriptomics and gene fusion analyses of a cohort of BCP-LBL and extramedullary (EM) manifestations of B-ALL patients, we performed RNA sequencing of 16 tissue samples from BCP-LBL and EM B-ALL patients. Because the material was available as FFPE, and had a relative low quality, we used a capture-based approach, where NGS libraries obtained from total RNA were captured in 4-plex, using a whole exome capture panel.

  Dataset EGAD50000002047

• A single-cell atlas of the early COPD lung

  Single cell atlas of the human airways from 10 patients suffering of early stage Chronic Obstructive Pulmonary Disease and 12 healthy age matched volunteers. This dataset was sequenced by 10X Genomics 3’ RNA-seq profiling. It is composed of more than 400 000 cells coming from 119 samples total. Sampling was performed by brushings and biopsies from the nose to the 6 th division of the airways.

  Dataset EGAD50000001001

• Oral microbiota composition assessed with 16S rRNA sequencing from adults aged over 65 years old.

  This is a oral microbiota amplicon dataset derived from adult participants aged over 65 years old. It consists a total number of 491 samples, stored in 982 paired-end FASTQ files with sequence lengths of 200 nucleotides generated with a Illumina MiSeq. Of those 491 samples, 347 were used in analysis, the remaining 144 samples are control samples.

  Dataset EGAD00001007705

• Whole Exome and RNA-Sequencing of Germline, Small Bowel Carcinoid Primary Tumor, and Liver Metastasis Trios

  This dataset includes trios of germline/constitutional, primary tumor (small bowel carcinoid), and metastatic tumor (liver) trios for 5 patients (i.e. 15 samples total). Constitutional, primary tumor, and metastatic tumor samples all underwent whole exome sequencing (WES or WXS). Primary and metastatic tumor samples underwent RNA sequencing (RNA-seq).

  Dataset EGAD00001010036

• Comprehensive RNA repository of tissue and plasma from patients with esophageal cancer or precursor lesions

  A comprehensive RNA repository (both coding and non-coding) from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were collected. This dataset includes both mRNA and small RNA sequencing data (fastq.gz files) of all tissue and plasma samples. In total,102 RNA-seq libraries from 51 samples (17 plasma and 34 tissue samples) were sequenced (plasma mRNA libraries were sequenced twice).

  Dataset EGAD00001006857

• RCC Infiltrated Macrophages and Monocytes

  Tumor infiltrated Macrophages and Monocytes were sorted on Aria II (Becton Dickinson) into TRIzol LS and flash frozen. RNA was extracted with chloroform. Isopropanol and linear acrylamide were added, and the RNA was precipitated with 75% ethanol. Total RNA (0.649–1 ng) with RNA integrity numbers 6.8 to 10 underwent amplification using the SMART-Seq v4. Ultra Low Input RNA Kit (Clontech; cat. #63488). Amplified cDNA (15 ng) was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems, KK8504) using 8 cycles of PCR.

  Dataset EGAD00001009393

• DNA-seq BAM files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by HPAH

  Paired-end DNA-seq BAM files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by hereditary pulmonary arterial hypertension (HPAH). Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). FASTQ files were processed at the CNAG (Barcelona) using the GEM short-read aligner on the human genome version hs37d5, producing a total of 16 BAM files.

  Dataset EGAD00001005757

• RNAseq on 20 samples of multiple myeloma patients and 3 normal plasma cells

  RNAseq on 20 samples of multiple myeloma patients and 3 normal plasma cells. RNAseq was performed using 200 ng of total RNA by GATC Biotech. Directional libraries were performed after mRNA selection by polyA selection using UTP method. RNA-seq libraries were sequenced on HiSeq2500 Illumina machine using 100bp paired-end reads. Reads alignment was performed using the STAR aligner (version 2.4.0f1) and human genome hg19 as reference.

  Dataset EGAD00001007813

• Sequencing data for rare tumors and sarcomas

  This dataset contains DNA and RNA sequencing information for AML, Gliomas, brain tumors (medulloblastoma and ependymoma), DIPG, rhabdoid tumors and soft tissue sarcomas. In total 39 samples are present (14 matched normal, 25 tumor samples). Not all samples have matched normals and not all samples have RNA sequencing data..

  Dataset EGAD00001008974

• Mitochondrial DNA sequencing of human iPSC, parental cells, and iPSC derived cardiomyocytes

  Dataset contains whole mitochondrial DNA sequencing data in fastq format (Illumina MiSeq paired-end) of 62 samples, in total. Those samples include sequencing data of the endothelial cell populations of 10 different donors and of 26 early-passage iPSC clones derived thereof. Moreover, the dataset contains the data of 7 of those iPSC clones sequenced additionally in passage 30 and 50, each. Lastly, 4 iPSC clones were sequenced during directed cardiomyocyte differentiation, each at day 0, 5, and 15 of differentiation.

  Dataset EGAD00001008021

• FFPE, buffycoat and cell free DNA from N. German esophagus cancer patients - 2021

  28 patients. Cell-free DNA and leukocyte DNA, both from before any neoadjuvant treatment. Tumor FFPE tissue (plus metastasic tissue for some patients) from after any neoadjuvant treatment. Some cfDNA from follow-up time points (e.g. after neodj. treatment or in the clinical course). IDT xgen Pan-Cancer panel for hybridisation capture. Illumina TruSeq library prep for cfDNA and leukocyte DNA, Illumina DNA Prep for FFPE DNA. n=150 libraries in total.

  Dataset EGAD00001010081

• Comparison of protocols for deriving pancreatic progenitors from hPSCs (ATAC-seq)

  This dataset contains 27 mapped bam files. The samples were generated with 3 different protocols for deriving pancreatic progenitors from hPSC. Three parallel differentiations were performed, all done in a hPSC NKX6.1-GFP reporter line. For each protocol there are three cellular populations: total (presort), GFP+ and GFP- . In summary: 3 differentiations x 3 protocols x 3 cellular populations. We prepared ATAC-seq libraries for the 27 samples, and sequenced them on Illumina HiSeq4000.

  Dataset EGAD00001004824

• Comparison of 3 protocols for deriving pancreatic progenitors from hPSCs (RNA-seq)

  This dataset contains 26 mapped bam files. The samples were generated with 3 different protocols for deriving pancreatic progenitors from hPSC. Three parallel differentiations were performed, all done in a hPSC NKX6.1-GFP reporter line. For each protocol there are three cellular populations: total (presort), GFP+ and GFP- . In summary: 3 differentiations x 3 protocols x 3 cellular populations. We prepared Smart-Seq2 RNA-seq libraries for the 27 samples, 1 sample failed library preparation and is not therefore included in this dataset.

  Dataset EGAD00001004823

• WES data from 165 tumor/germline samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). WES was performed using DNA from 165 tumors (76x median coverage) and associated germline DNA (46x median coverage). Data provided here consist of 5,828 fastq files for WES.

  Dataset EGAD00001006239

• VCF file from 16 patients affected by acute intermittent porphyria

  VCF file from 16 patients affected by acute intermittent porphyria. Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). BAM files were processed at the CNAG (Barcelona) with their pipeline, including GATK v3.6 for genotyping and other tools such as snpEff for annotating variants, to produce this VCF file with a total of 10,630,259 variants, out of which 8,731,523 are SNVs.

  Dataset EGAD00001006952

• RNAseq of human fetal pancreas development

  The dataset comprises RNA-seq information of 4 subpopulations sorted from human fetal pancreas of 3 different donors. Low input libraries were generated using the Smart-seq2 protocol after Ampure XP cleanup of the total RNA extracted from the sorted cells. Libraries were multiplexed and sequenced paired-end over 2 lanes of HiSeq4000 each. Raw data was aligned to the human genome refernence GRCh37 using STAR v2.5.1b with GENCODE v19 as transcriptome reference, and unaligned reads were folded into the final uploaded bams.

  Dataset EGAD00001004210

• Multiple myeloma Total Therapy trial patient sequencing

  DNA was obtained from either CD138+ cells from the bone marrow of multiple myeloma patients (tumor) or from stem cell harvests or peripheral blood cells from the same patient (control). 100 ng of DNA was fragmented, end-repaired, and adapters ligated using the HyperPlus kit (KAPA Biosystems). After PCR amplification the libraries were hybridized with probes against either a targeted panel consisting of 140 genes and chromosomal regions (Nimblegen) using SeqCap reagents (Nimblegen). Hybridized libraries underwent further amplification before being sequenced on a NextSeq500 (Illumina) using 75 bp paired end reads.

  Dataset EGAD00001004373

• RNA-Seq of patient-derived fibroblast cell lines with inborn errors of cobalamin (vitamin B12) metabolism and controls

  RNA sequencing of 31 patient-derived fibroblast cell lines from patients with inborn errors of cobalamin (vitamin B12) metabolism, and 7 control samples. The RNA seq library was prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina RS-122–2301) including Ribo-Zero Gold depletion to remove ribosomal RNA. Sequencing was done via llumina Hi-Seq2000 sequencer, using 100bp paired end reads.

  Dataset EGAD00001003142

• Whole transcriptome sequencing of Acute Myeloid Leukemias with an acquired inv(3)(q21q26) or t(3;3)(q21;q26) aberration

  In total 30 Acute Myeloid Leukemias with an acquired inv(3)(q21q26) or t(3;3)(q21;q26) have been characterized by whole transcriptome sequencing (RNA-Seq). The 3q-aberration leads to overexpression of the proto-oncogene EVI1, but the mechanism of overexpression has thus far been elusive. The RNA-Seq was integral in determining the precise enhancer inducing the overexpression and led to other key discoveries.

  Dataset EGAD00001000726

• Raw FASTQ files from TSO500 hybrid capture sequencing of prostate cancer tissue and plasma.

  This dataset contains raw genomic sequencing data in FASTQ format for a total of 49 libraries. It includes 22 samples derived from formalin-fixed paraffin-embedded (FFPE) tissue and 27 samples from plasma cell-free DNA (cfDNA). All samples were processed using the Illumina TruSight Oncology 500 (TSO500) hybrid capture panel to identify relevant genomic alterations. These files represent the primary, non-aligned data used for the comparative performance analysis described in the associated study.

  Dataset EGAD50000002463

• Single-nucleus RNA sequencing (snRNA-seq) of seven human diffuse midline glioma (DMG) patient tumour samples.

  This dataset comprises 7 paired (14 total) FASTQ files of single-nucleus RNA sequencing (snRNA-seq) data generated from seven human diffuse midline glioma (DMG) patient tumour samples. snRNA-seq libraries were generated using the 10X Chromium Controller and Chromium Next GEM Single Cell 3’ kit version 3.1 in line with the manufacturer’s instructions. Generated libraries were sequenced on an Illumina NextSeq 2000 (P3 XLEAP-SBS chemistry) at targeted 20,000 reads per nucleus.

  Dataset EGAD50000002514