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• Women's Health Study Accelerometry Dataset

  Background The Women's Health Study (WHS) was a randomized trial testing low-dose aspirin and vitamin E for preventing cancer and CVD among 39,876 women aged ≥45 years throughout the US from 1992-2004. When the trial ended as planned, women who were willing to participate continued in an observational follow-up study. Participants in Accelerometer Study From 2011-2015, an ancillary study collected data on physical activity and sedentary behavior using accelerometers. Women were mailed a triaxial accelerometer (ActiGraph GT3X+, ActiGraph Corp) with a wear log, and asked to wear this on their hip for seven consecutive days, removing it only during sleep and water-based activities. Further details have previously been published (PMID: 30666321). A total of 17,708 women wore and returned their devices, and data were downloaded from the devices of 17,466 women; no data were available from the other 242 (device failure). By convention, a "valid day" of wear has data on at least 10 hours (PMID: 22698174). Among these 17,466 women, 17,062 had at least one valid day of wear. The data are provided for all 17,062 women. Additionally, "compliant wear" is conventionally defined for participants wearing the device for at least 10 hours, on at least 4 days (PMID: 22698174). Of the 17,062 women, 16,741 had compliant wear (PMID: 29109088). Self-reported Physical Activity and Sedentary Behavior After we received the accelerometer from a WHS participant, she was sent a questionnaire asking her to report the time she spent in different physical activities during the week that the accelerometer was worn (see questionnaire below). A total of 15,514 women (91% of participants in the Accelerometer Study) returned their physical activity questionnaires. In addition, beginning in October 2012, we included questions on sedentary behavior; a total of 9,430 women returned questionnaires that included questions on both physical activity and sedentary behavior.

  Study phs001964

• SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues

  SARS-CoV2 mRNA vaccination-induced CD4+ Th cells were isolated based on activation marker expression from human bone marrow (n=3), lung (n=5), liver (n=4) and paired blood samples (to liver donors, n=4) of virus-naive vaccinees after Spike peptide mix stimulation in vitro. The 10X platform was used for single cell transcriptome analysis, along with T cell receptor clonotype analysis in a total of 1985 cells. Samples were sequenced on a NovaSeq 6000 (Illumina).

  Study EGAS50000000045

• Characterization of the Gut-Associated Microbiome in Inflammatory Pouch Complications Following Ileal Pouch-Anal Anastomosis

  This study involved evaluation of the tissue associated microbiome of the ileal pouch following surgery for ulcerative colitis (UC) or familial adenomatous polyposis (FAP). Individuals were recruited, with biopsies taken from the ileal pouch and the pre-pouch ileum, microbial DNA was extracted and sequenced using 454 pyrosequencing. Total bacterial community structure and abundance were evaluated to determine which changes were characteristic of inflammatory phenotypes including pouchitis (inflammation of the ileal pouch) and a Crohn's disease-like phenotype.

  Study phs000659

• RNA sequencing from patient-derived intestinal organoids

  RNA from the duodenal organoids was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA purity and concentration were measured using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). Preparation of the RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Cambridge, UK). Messenger RNA was purified from total RNA using polyA selection and subjected to library construction. Sequencing was performed on an Illumina platform, and 150 bp paired-end reads were generated.

  Study EGAS50000000338

• Activation-Induced Marker (AIM) Sequencing of Healthy Human T Cells

  T cells from five healthy human donors were stimulated with a peptide pool (CEFX, JPT) and anti-CD28/CD49d co-stimulation. Cells were then sorted based on activation (OX40 and PD-L1 for CD4s, CD137 for CD8s) and labeled with corresponding hashing antibodies prior to sequencing. In total, this dataset encompasses 42,370 cells (12,743 activation-induced marker (AIM)-positive, 15,369 AIM-negative, 14,258 Mock) for CITE-sequencing and TCR-sequencing of sorted activated, unactivated, and mock T cells derived from blood.

  Study phs004043

• Emirati Phased Diploid Trio-Assemblies

  This study, conducted under the Emirati Genome Project, aims to build a foundational pangenome reference to enable precision medicine in the United Arab Emirates. We generated phased diploid genome assemblies for 27 Emirati nationals using deep PacBio HiFi sequencing and a trio-based assembly procedure. In total, this produced 54 haplotype-resolved assemblies representing maternal and paternal genomes for each participant. The resulting high-quality reference captures population-specific genetic diversity and will accelerate translational research, variant interpretation, and genome-informed healthcare in the region.

  Study EGAS50000001234

• Genome-wide SNP data of Fulani populations from the Sahel belt

  This project seeks to uncover the genetic structure and ancestry of the Fulani populations across the Sahel/Savannah Belt. The study includes two datasets (''WGA_Fulani_Database'' and ''Saliva_Fulani_Ddatabase''), and SNP-genotyping data was generated using the Illumina Infinium H3Africa Consortium array (BeadChip type: H3Africa_2019_20037295_B1) in two genotyping batches (TE-2559_201029 and TE-2559_201020). In total, 419 were genotyped for this study and the key results were presented in Fortes-Lima et al. 2024 (doi: 10.1101/2024.06.22.600206).

  Study EGAS50000000451

• RNA sequencing of CD8 T cells from melanoma patients prior to and during checkpoint immunotherapy and untreated healthy controls

  We are interested in inter-individual variation in transcriptional response to immune checkpoint blockade. We have analysed poly A purified RNA expression from CD8 T cells (297 transcriptomes in total) isolated from metastatic melanoma patients (n=106) prior to and during treatment with either single agent (Pembrolizumab) or combination (Ipilimumab/ Nivolumab) immune checkpoint blockade. We compare expression at different stages of treatment and additionally contrast this with that from healthy controls (n=68).

  Study EGAS00001004081

• LCM-ATACseq on human lung macrophages

  In this study we employed Laser Capture Microdissection (LCM) for the multimodal profiling of lung macrophages cell populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (~100 cells) were collected from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 – lower left lobe (LLL); L6 – 80% distance from LLL tip), trachea (L2), bronchi (L3 – 1st/2nd generation; L5 – 3rd/4th generation), and processed for ATAC-seq.

  Study EGAS00001006167

• Hip OA Functional Genomics

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of hip osteoarthritis that culminates in the need for total joint replacement (TJR). This study is a feasibility pilot that integrates functional genomics data from diseased and non-diseased tissues of OA patients who have undergone TJR. For each tissue, we characterised epigenetic marks (methylation), gene transcription (RNASeq) and expression (quantitative proteomics). We also generated genotype data on the HumanCoreExome array for each individual.

  Study EGAS00001002483

• SNP arrays for chemotherapy response project

  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). Illumina SNP arrays (760k markers) were performed using DNA from 49 tumors and associated germline DNA (49x median coverage). Data provided here consist of 98 files.

  Study EGAS00001004519

• Targeted_sequencing_of_genes_recurrently_mutated_in_AML___part2

  Genomic libraries will be generated from total genomic DNA derived from 4000 samples with Acute Myeloid Leukaemia. Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 64 Samples will be individually barcoded and subjected to up to one lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.

  Study EGAS00001000570

• Knee_OA_Functional_Genomics

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of knee osteoarthritis that culminates in the need for total joint replacement (TJR). This study is a feasibility pilot that integrates functional genomics data from diseased and non-diseased tissues of OA patients who have undergone TJR. For each tissue, we characterised epigenetic marks (methylation), gene transcription (RNASeq) and expression (quantitative proteomics). We also generated genotype data on the HumanCoreExome array for each individual.

  Study EGAS00001001899

• The WID-CIN test identifies women with, and at risk of, cervical intraepithelial neoplasia grade 3 and invasive cervical cancer (CIN3+)

  We analysed DNA methylation at >850,000 CpG sites across the genome using the Illumina EPIC array in a total of 1,254 cervical liquid-based cytology samples from cases of screen-detected histologically verified CIN1-3+ (98% hrHPV-positive) and population-based control women free from any cervical disease (100% hrHPV-positive). We developed the WID-CIN-test which is a DNA methylation signature consisting of 5,000 CpG sites.

  Study EGAS00001005078

• DGCR8 and the six hit, three-step model of schwannomatosis

  In our manuscript, we report the second case of a patient with peripheral schwannomatosis and thyroid alterations cause by the germline pathogenic variant E518K in DGCR8 and analyzed a total of 13 schwannomas from patients in the two kindreds identified up to date. Our analyses revealed how path to tumorigenesis prompted by DGCR8 requires the loss of the wild type allele of Chrm22q and in more than two thirds of the tumors a complete inactivation of NF2.

  Study EGAS00001005665

• LCM-RNAseq on human lung macrophages

  In the reported study, we employed Laser Capture Microdissection (LCM) for the transcriptome profiling of lung macrophages cells populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (100 cells each) were collected by LCM from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 – lower left lobe (LLL); L6 – 80% distance from LLL tip), trachea (L2), bronchi (L3 – 1st/2nd generation; L5 – 3rd/4th generation) and processed for RNA-seq.

  Study EGAS00001006168

• Tissue DNA, WBC DNA and cfDNA (deep-)sequencing of mCRC patients treated with doublet chemotherapy and anti-EGFR in the CAIRO5 study

  This study assessed whether ctDNA based treatment response monitoring could be performed in a tumor tissue-independent manner by combining ultra-deep targeted sequencing analyses of cfDNA with patient-matched white blood cell (WBC) derived DNA. In total, 183 cfDNA and 49 WBC samples, along with 28 tissue samples, from 52 metastatic colorectal cancer patients participating in the prospective phase III CAIRO5 clinical trial (NCT02162563) were analyzed using the PGDx elio plasma resolve assay.

  Study EGAS00001006695

• Cold Ischemia Study

  This study aimed to evaluate the impact of cold ischemia time on the expression of cancer-related genes, particularly those involved in hypoxia, apoptosis, and epithelial-to-mesenchymal transition (EMT). We performed RNA sequencing on 54 normal colon mucosa samples from nine patients undergoing colorectal cancer surgeries, freezing samples at predefined intervals ranging from 0 to 60 minutes. A total of 44 differentially expressed genes (DEGs) (p < 0.05) were identified when comparing samples frozen immediately (T0) with those frozen after 60 minutes (T5).

  Study EGAS00001008233

• RNA-seq FASTQ files from newborn screening dried blood spot samples

  Paired-end RNA-seq FASTQ files from 21 newborn screening dried blood spot (DBS) samples. These DBS samples were obtained from extremely low gestional age newborns, where 10 of them were affected by a fetal inflammatory response (FIR) before birth, and 11 were unaffected. Total RNA was sequenced using an Illumina NextSeq-500 instrument. The sample preparation protocol included the depletion of rRNA and globin mRNA using the Globin Zero Gold rRNA Removal Kit from Illumina. Libraries were prepared using the NebNext Ultra TM II Directionl RNA LIbrary Prep Kit (New England Biolabs). Each sample was sequenced in 4 lanes, leading to 8 FASTQ files per sample and a total of 21x8=168 FASTQ files. There is an additional number of 8 FASTQ files corresponding to sample BS13, which was downsampled to 1/4 of its original depth (see BS13_README file for details).

  Dataset EGAD00001004991

• Patient tumour data (RNAseq, WGBS, ChIPseq, WGS)

  Content: 60 GB patient tumours and 4 normal brain samples combined in pairs by region (x2=8 total input samples). RNAseq: 1 lane per sample, total strand-specific rRNA-depleted (normal samples were combined = 2 lanes/samples per brain region). WGBS: 2 lanes per sample (normal samples were combined = 2 lanes/samples per brain region). ChIPseq (histone mark): a subset of 20 GB samples were profiled. For the same modification were multiplexed and sequenced on 4 lanes each (H3K27ac, H3K4me1) or a single lane (all others). WGS: used as matching input control for the 20 ChIPseq samples. Data type and technology: RNA-seq: PE 100bp sequenced on HiSeq2000. WGBS: PE 100bp sequenced on HiSeq2000/4000. ChIPseq: SE 50bp sequenced on HiSeq2000/4000. WGS: PE 150bp sequenced on HiSeq X.

  Dataset EGAD00001005492

• Total XVI RNAseq

  RNAseq data of total TXVI samples

  Dataset EGAD00001007530

• WGS and WTS data of patients diagnosed with MEITL.

  WGS from 4 patients, WTS from only 3 patients (insufficient tissue from 4th patient for WTS). Whole-genome sequencing (WGS) was performed for 60 pairs of tumor-normal samples from patients diagnosed with NKTL. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 2000. Whole-transcriptome sequencing (WTS): Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on Illumina HiSeq 2500 with 2x101 bp read length. Description of prefix used in filenames: T: Tumor samples N: Normal samples (Blood) P: PDX samples

  Dataset EGAD00001005341

• Transcriptome-wide gene expression analysis of cocaine use disorder in postmortem human brain tissue

  Dataset contains raw fastq-files from RNA-sequencing analysis of total RNA extracted from Brodmann Area 9 human postmortem brain tissue samples.

  Dataset EGAD50000000212

• NICHE - RNA-seq of MMR proficient early stage colon cancers

  The dataset includes 29 FASTQ files from single-end total RNA sequencing on Illumina HiSeq2500 and 66 files from 33 paired-end RNA sequencing samples on Novaseq 6000 for 31 pMMR colon cancer patients.

  Dataset EGAD50000001248

• Dual RNA-seq data of chlamydia infected M2 macrophages

  This dataset contains 8 unpaired fastq files sequenced with Ilumina NextSeq 2000. The files contain transcriptome data of host and pathogen from infected and uninfected samples from extracted total RNA at 30 hours post infection.

  Dataset EGAD50000001398

• Sporadic and endemic Burkitt lymphoma have frequent FOXO1 mutations but distinct hotspots in the AKT recognition motif

  Sample set of 74 whole-exome sequencing samples from sporadic Burkitt lymphoma patients from the UK. 33 of these samples have matched constitutional data, giving a total number of 107 samples

  Dataset EGAD00001005105

• Gene expression in human monocyte differentiation

  This dataset consists of RNA-seq data data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting TET2, IRF4 and EGR2. In total, it includes 43 samples.

  Dataset EGAD00001006604

• Pre and Post BCG treated bulk RNAseq dataset.

  We have in total 16 files, technical duplicates of 8 unique samples from Pre and Post BCG samples collected from four non muscle invasive bladder cancer patients. These are bulk RNAseq samples generated by high-throughput sequencing platform.

  Dataset EGAD00001006634

• Transcriptome analysis of Treg cells from blood, fat, liver and skin

  Tcells were isolated fom Tissues and FACS sorted. In total 43 samples were processed in 5 replicates with the Takara SmartSeq Stranded kit. Single end fastq-files are supplied.

  Dataset EGAD00001007664

• Transcription factor binding in human monocyte differentiation

  This dataset consists of ChIP-seq data data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to mRNA transfection for PU.1, IRF4, and EGR2. In total, it the data set includes 18 samples.

  Dataset EGAD00001006602

• Chromatin accessibility in human monocyte differentiation

  This dataset consists of ATAC-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting TET2, IRF4 and EGR2. In total, it includes 26 samples.

  Dataset EGAD00001006601

• Gene expression in LPS-stimulated human monocyte-derived macrophages

  This dataset consists of RNA-seq data from human monocyte-derived macrophages that were subjected to siRNA treatment targeting RAD21 and either left untreated, or stimulated with LPS. In total, it includes 24 samples.

  Dataset EGAD00001007952

• Epigentic sequence data of monocytes and macrophages

  Data for paper: Epigenetic dynamics of monocyte to macrophage differentiation with Chip Seq, NOMe, mRNA, total RNA, noncoding RNA, whole genome bisulfite seq,

  Dataset EGAD00001002201

• Neuroblastoma deep-sequencing dataset part2

  Dataset including paired tumor-normal whole-genome deep-sequenced samples from 18 neuroblastoma patients (part 2 of a total of 36 patients).

  Dataset EGAD00001010063

• Bulk RNA from sorted CD8+ T cells after 48h co-culture with human Mito-DsRed MSCs.

  For human samples, total cellular RNA was isolated from post-sorted Mito+ and Mito CD8+ cells using the RNeasy Mini Kit (Qiagen). Stranded RNA libraries were created using SMARTSeq Stranded.

  Dataset EGAD00001011082

• RNA-seq colorectal adenomas NKI-AvL TGO series NGS-ProToCol

  The dataset "RNA-seq colorectal adenomas NKI-AvL TGO series NGS-ProToCol" includes 2 x 30 fastq files from paired-end total RNA sequencing on Illumina HiSeq2500 for 30 snap-frozen colorectal adenomas.

  Dataset EGAD00001004055

• RNA-seq colorectal carcinomas NKI-AvL TGO series NGS-ProToCol

  The dataset "RNA-seq colorectal carcinomas NKI-AvL TGO series NGS-ProToCol" includes 2 x 30 fastq files from paired-end total RNA sequencing on Illumina HiSeq2500 for 30 snap-frozen colorectal carcinomas.

  Dataset EGAD00001004056

• Cardiac Translatomes of 80 Human Samples

  Dataset consists of fastq files of Ribo-seq, polyA-RNA and total RNA sequencing of 80 samples (65 DCM cases and 15 controls)

  Dataset EGAD00001004394

• Deep-Seq: Resistance to anti-EGFR therapy in colorectal cancer

  In this study we performed ultra deep sequencing of genes associated with anti-EGFR resistance, such as KRAS, BRAF, PIK3CA, and EGFR in 17 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy.

  Dataset EGAD00001000688

• Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Lipidomics Study

  The GOLDN study was initiated to assess how genetic factors interact with environmental (diet and drug) interventions to influence blood levels of triglycerides and other atherogenic lipid species and inflammation markers (registered at clinicaltrails.gov, number NCT00083369). The study recruited Caucasian participants primarily from three-generational pedigrees from two NHLBI Family Heart Study (FHS) field centers (Minneapolis, MN and Salt Lake City, UT). Only families with at least two siblings were recruited and only participants who did not take lipid-lowering agents (pharmaceuticals or nutraceuticals) for at least 4 weeks prior to the initial visit were included. A total of 1048 GOLDN participants were included in the diet intervention. The diet intervention followed the protocol of Patsch et al. (1992). The whipping cream (83% fat) meal had 700 Calories/m2 body surface area (2.93 MJ/m2 body surface area): 3% of calories were derived from protein (instant nonfat dry milk) and 14% from carbohydrate (sugar). The ratio of polyunsaturated to saturated fat was 0.06 and the cholesterol content of the average meal was 240 mg. The mixture was blended with ice and flavorings. Blood samples were drawn immediately before (fasting) and at 3.5 and 6 hours after consuming the high-fat meal. For the GOLDN lipidomics study, sterols and fatty acids were measured from stored plasma (-80 degrees Celsius) collected at fasting and 3.5 hours after the diet intervention using TrueMass Panels from Lipomics (West Sacramento, CA). A total of 11 sterols were quantified in nmols/gram of sample including total cholesterol, 7-dehydrocholesterol, desmosterol, lanosterol, lathasterol, cholestanol, coprostanol, beta-sitosterol, campesterol, stigmasterol, and 7alpha-hydroxycholesterol. A total of 35 fatty acids were quantified in nmols/gram of sample inlcuding myristic acid (14:0); pentadecanoic acid (15:0); palmitic acid (16:0); stearic acid (18:0); arachidic acid (20:0); behenic acid (22:0); lignoceric acid (24:0); myristoleic acid (14:1n5); palmitoleic acid (16:1n7); palmitelaidic acid (t16:1n7); oleic acid (18:1n9); elaidic acid (t18:1n9); vaccenic acid (18:1n7); linoleic acid (18:2n6); gamma-linolenic acid (18:3n6); alpha-linolenic acid (18:3n3); stearidonic acid (18:4n3); eicosenoic acid (20:1n9); eicosadienoic acid (20:2n6); mead acid (20:3n9); di-homo-gamma-linolenic acid (20:3n6); arachidonic acid (20:4n6); eicsoatetraenoic acid (20:4n3); eicosapentaenoic acid (20:5n3); erucic acid (22:1n9); docosadienoic acid (22:2n6); adrenic acid (22:4n6); docosapentaenoic acid (22:5n6); docosapentaenoic acid (22:5n3); docosahexaenoic acid (22:6n3); nervonic acid (24:1n9); and plasmalogen derivatives of 16:0, 18:0, 18:1n9, and 18:1n7.

  Study phs000741

• Whole Transcriptome Sequencing of Human Tumor Cells and Hematopoietic Stem and Progenitor Cells During Aging and Bone Marrow Disorders

  Whole transcriptome sequencing analyses were performed on human hematopoietic stem and progenitor cells during aging and bone marrow disorders. For this purpose, normal and diseased bone marrow or peripheral blood-derived mononuclear cells were FACS-purified into hematopoietic stem (CD34+CD38-Lin-) or hematopoietic progenitor (CD34+CD38+Lin-) populations. Primary human samples from healthy individuals were used along with comparative analyses in some pre-malignant and malignant conditions, including myelodysplastic syndrome (MDS), acute myeloid leukemia (AML) and plasma cell dyscrasias (e.g., multiple myeloma). Studies were also performed on total mononuclear cell fractions from patients with newly-diagnosed or relapsed multiple myeloma, or plasma cell leukemia. Briefly, RNA was extracted from all samples and quality was assessed using a Bioanalyzer instrument. Only samples with RNA integrity (RIN) values >7 were subjected to library preparation for RNA-sequencing. The SMARTer v4 cDNA amplification kit was used along with library construction by the NEB Ultra DNA kit for Illumina. Paired-end sequencing was performed on Illumina NextSeq instruments (Scripps Next Generation Sequencing Core), with all samples run over two separate flow-cells (to generate additional sequencing reads); >95M reads were generated in total for each sample. The RNA-sequencing data are available as FASTQ files.

  Study phs002291

• Assessing gene expression profiling from FFPE Patient Samples: A Comparison of Two Library Preparation Approaches and Recommendations

  Next-Generation Sequencing (NGS) has transformed cancer research and clinical practice, with Whole Exome Sequencing (WES) driving advances in mutational profiling and personalized oncology. Yet, transcriptomic signatures remain essential for understanding disease mechanisms, including therapy resistance pathways. RNA sequencing (RNA-seq), however, faces unique challenges when dealing with low-input or degraded RNA, as often found in archival formalin-fixed paraffin-embedded (FFPE) tissues. Although previous studies have compared library preparation protocols, rapidly evolving technologies call for updated evaluations. Here, we present a direct comparison of two FFPE-compatible stranded RNA-seq library preparation kits: TaKaRa™ SMARTer® Stranded Total RNA-Seq Kit v2 (Kit A) and Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Kit B). Both kits generated high-quality RNA-seq data, yet important differences emerged. Notably, Kit A achieved comparable gene expression quantification to Kit B while requiring 20-fold less RNA input, a crucial advantage for limited samples, albeit with increased sequencing depth. We critically discuss these results in relation to RNA availability, technical performance, cost-effectiveness, processing time, and automation potential, offering practical guidance for selecting optimal RNA-seq strategies in clinical and translational research settings

  Study EGAS50000001066

• FASTQ files of total RNA-Seq data from the POPS PET (pre-eclamptic) samples

  All the samples were obtained from the Pregnancy Outcome Prediction–a prospective cohort study of nulliparous women attending the Rosie Hospital, Cambridge (UK) for their dating ultrasound scan between January 14, 2008, and July 31, 2012. Ethical approval for the study was given by the Cambridgeshire 2 Research Ethics Committee (reference number 07/H0308/163) and all participants provided written informed consent. Cases of preeclampsia (PET) were defined on the basis of the 2013 ACOG criteria and cases of small for gestational age (SGA)infants were confined to severe SGA, i.e. a customized birth weight <5th percentile. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

  Dataset EGAD00001003508

• FASTQ files of total RNA-Seq data from the POPS SGA (Small for Gestational Age) samples

  All the samples were obtained from the Pregnancy Outcome Prediction–a prospective cohort study of nulliparous women attending the Rosie Hospital, Cambridge (UK) for their dating ultrasound scan between January 14, 2008, and July 31, 2012. Ethical approval for the study was given by the Cambridgeshire 2 Research Ethics Committee (reference number 07/H0308/163) and all participants provided written informed consent. Cases of preeclampsia (PET) were defined on the basis of the 2013 ACOG criteria and cases of small for gestational age (SGA)infants were confined to severe SGA, i.e. a customized birth weight <5th percentile. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

  Dataset EGAD00001003507

• Enrichment Data

  Fresh fecal samples were donated from healthy individuals. We evaluated the responses of healthy adult fecal microbiota to distinct carbon source conditions, pH levels and redox potentials. Metabolite concentrations were measured by HPLC. The total genomic DNA was extracted, sequenced and analyzed. The research project was approved by the Ethic Committee of the Canton of Zurich (2017-01290).

  Dac EGAC50000000346

• RNAseq dataset of ovarian cancer patients

  Dataset of transcriptomics data from a cohort of individuals diagnosed with ovarian cancer. This dataset includes RNAseq sequencing data from 68 individuals. A total of 109 tumor samples were sequenced. Samples were prepared with the Illumina TruSeq Stranded RNA library. Sequencing data are paired end.

  Dataset EGAD50000001556

• Chromatin accessibility in human monocytes differentiation

  This dataset consists of ATAC-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, it includes 39 samples.

  Dataset EGAD00001007953

• RNAseq of SCCOHT patient tumors

  This data set contains BAM files of the RNAseq analysis for three SCCOHT patient tumors. Total mRNA was isolated from fresh frozen tumor samples. RNA sequencing was performed using Illumina HiSeq 4000, paired end 150 bp.

  Dataset EGAD00001007829

• Spatial transcriptome sequence data from prostate cancer needle biopsies

  Spatial transcriptome sequencing data from prostate cancer needle biopsies. Dataset contains biopsies from before and after androgen deprivation therapy of 3 patients with 8 biopsies per patient in total. 2 sections (replicates) are taken from each biopsy.

  Dataset EGAD00001008636

• Whole-exome sequencing and microRNA profiling predicted relapse risk of stage I lung adenocarcinomas

  This dataset contains BAM files for whole exome-sequencing of stage I lung adenocarcinomas from Asian patients. In total, there are 113 patients and 262 samples, including 113 tumor samples, 113 adjacent normal samples and 36 buffy coat samples.

  Dataset EGAD00001006188

• Single cell Transcriptome Analysis of regulatory Tcells from blood, fat and skin

  Regulatory Tcells were FACS sorted and processed with 10x Genomics Chromium Next GEM Single Cell 5' v2 sequencing. In total 17 samples were processed. Fastq files are supplied.

  Dataset EGAD00001007665

• ACC RNASeq data

  Samples prepared using TruSeq Stranded Total RNA library kit. Samples sequenced on a HiSeq 2000.

  Dataset EGAD00001008192

• Targeted sequencing of breast cancer susceptibility genes for 1,995 Japanese breast cancer patients

  This dataset consists of 106 bam files. Each sample from 10-20 consecutive patient extractions were combined into one DNA pool, generating a total of 106 DNA pools. We sequenced 11 genes implicated in hereditary breast cancer using the SureSelect Custom kit.

  Dataset EGAD00001006368

• RNA-seq normal adjacent colon NKI-AvL TGO series NGS-ProToCol

  The dataset "RNA-seq normal adjacent colon NKI-AvL TGO series NGS-ProToCol" includes 2 x 18 fastq files from paired-end total RNA sequencing on Illumina HiSeq2500 for 18 snap-frozen normal adjacent colon tissues.

  Dataset EGAD00001004057

• Somatic mutations in epithelial cells from endometriosis and normal uterine endometrium

  Somatic mutations in epithelial cells from endometriosis and normal uterine endometrium, with a total of 24 samples. Target enrichment was conducted by Agilent SureSelect Human All Exon V5 + IncRNA kit. Sequencing was conducted by Illumina HiSeq 2500 platform. Somatic mutation call was performed by Strelka.

  Dataset EGAD00001004186

• TRACERx esophageal adenocarcinoma multi-region NGS

  This dataset contains whole exome data from 8 esophageal adenocarcinoma tumors, that has been subjected to multiregion sequencing, ranging from 3-8 regions per tumor. In total, 40 tumor samples and 8 normal blood samples have been sequenced on Illumina HiSeq 2500 at a median dept of 90x.

  Dataset EGAD00001001364

• Nurminen et al ("GP2Men") Study Primary and Metastatic Prostate Cancer Whole Genome Sequence Data

  We used novel processing techniques to obtain whole genome data together with 3D anatomic and histomorphologic analysis in two men (GP5 and GP12) with high risk PrCa undergoing radical prostatectomy. A total of 22 whole genome-sequenced sites (16 primary cancer foci and 6 lymph node metastatic) were analyzed using evolutionary reconstruction tools and spatio-evolutionary models. Probability models were used to trace spatial and chronological origins of the primary tumor and metastases, chart their genetic drivers, and distinguish metastatic and non-metastatic subclones.

  Study EGAS50000000005

• Avelumab or M7824 for People with Recurrent Respiratory Papillomatosis

  This submission includes genomic data derived from the study of clinical samples from two different phase II trials. These trials evaluated the clinical efficacy and safety of avelumab or M7824 in the treatment of adults with recurrent respiratory papillomatosis (RRP). Subjects with aggressive RRP were treated with three to six doses of avelumab or M7824. Pre-treatment or post-treatment snap frozen papilloma and normal mucosa samples were subjected to whole exome sequencing and bulk RNA-seq. A total of twenty subjects were enrolled and treated. 

  Study phs002373

• Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure (InterGEN Study)

  This research study focuses on the genomic and psychological environmental effects on blood pressure among mothers and their children. The study includes 250 mothers who self-identify as AA/black, and 250 children between the ages of 3 and 5 years old at the time of enrollment. The study is longitudinal and data collection interviews are scheduled every six months for two years after enrollment, for a total of four participant interviews. Assessment is as follows: genetic (time 1 only) and psychological factors (every six months for two years).

  Study phs001792

• A Prospective Study of Lifestyle, the Gut Microbiome, and Diverticulitis

  By leveraging a large-scale collection of stool specimens (Micro-N) within the Nurses' Health Study II, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 case women with a diagnosis of diverticulitis requiring antibiotics or hospitalization, with each matched to a control woman without diverticulitis during the same time period accounting for age, race, and month of stool collection (total N=242). We found microbiome and metabolomic profiles differed in diverticulitis cases compared to controls. Data deposited include metagenomic sequencing data (after removing the human sequences) and metabolomics data.

  Study phs003531

• Alterations in the gut microbiome in inflammatory arthritis implicate key taxa and metabolic pathways across arthritis phenotypes

  The gut microbiome has been implicated in several inflammatory conditions, but large-scale metagenomic evaluations have not yet traced the routes by which immunity in the gut affects systemic inflammatory diseases, such as inflammatory arthritis. To characterize the community structure and associated functional processes driving gut microbial involvement in arthritis, we investigated a total of 440 stool shotgun metagenomes comprising 275 adults diagnosed with rheumatoid arthritis, ankylosing spondylitis, or psoriatic arthritis, along with 165 healthy control individuals and individuals with joint pain without an underlying inflammatory cause.

  Study EGAS00001005525

• MIBC NAC2020 cohort RNA sequencing

  The dataset contains RNA sequencing data from N=48 transurethral resections of bladder tumours (TURBTs) from N=48 patients with muscle-invasive bladder cancer. All TURBTs originate from formalin-fixed paraffin embedded tissue. We used the Illumina TruSeq RNA exome kit, previously known as the TruSeq RNA Access Library Prep Kit. This kit converts total RNA into template molecules of known strand origin, followed by sequence-specific capture of coding RNA. All samples were run in an Illumina NovaSeq6000 instrument. Paired FASTQ files from all 48 patients are provided.

  Study EGAS50000000741

• Effects of Metformin on Transcriptomic and Metabolomic Profiles in Breast Cancer Survivors Enrolled in the Randomized Placebo-Controlled MetBreCS Trial

  RNA from snap-frozen breast tissue biopsies were purified after lysing by tissuelyser (Qiagen) and using RNA Purification Plus Kit (Norgen biotek CORP, 47700) with additional on-column DNase-I treatment (Qiagen, 79254) at 27 °C. RNA purity and integrity (RIN) were quantified using RNA 6000 Nano kit (Agilent Technologies, 5067-1511) on the 4200 TapeStation (Agilent, Santa Clara, USA). Library preparation and 2x75bp paired-end of 160 ng total RNA input was performed using Illumina Stranded Total RNA Prep Ligation kit and Illumina HiSeq4000 system (Illumina, Sand Diego, CA, USA). RNA sequencing data from HiSeq4000 were quality checked and aligned to GRCh38 (GCA_000001405.15) reference genome using HISAT2 2.0.5 and submitted to subread v.1.5.2 for feature counts calculation. Finally, 36 paired biopsies samples (metformin n=26 and placebo n=12) were sequenced and included in the final analyses.

  Dataset EGAD50000001274

• Other NS tumors

  The dataset represents a total of 18 DNA samples from 6 male and 3 female pediatric patients affected with central or peripheral nervous system tumors not classified as embryonal central nervous system tumors, nor gliomas, glioneuronal, or neuronal tumors. One tumor tissue sample and one peripheral blood sample from each patient were subject to whole genome sequencing (WGS) and were sequenced 2x150 bp paired-end on an Illumina HiSeqX v2.5 instrument. The FASTQ files generated were aligned to the human reference genome sequence GRCh38/hg38 using bwa-mem, with the ALT-aware option turned on. Sorting of reads and marking of PCR duplicates was performed with GATK. Base quality score recalibration and joint realignment of reads around insertions and deletions (indels) were conducted using GATK tools. The dataset consists of 18 files in the CRAM format (lossless compression) with a total file size of ~3,4 TB. Additional genomic and molecular data (FASTQ, BAM, IDAT, and VCF files) and limited clinical data can be requested by ethically approved projects conducting research in the field of pediatric cancer.

  Dataset EGAD50000000299

• Multi-Omics Study of Lung Cancer in Smokers From EAGLE

  EAGLE (Environment And Genetics in Lung cancer Etiology) is a population-based case-control study examining the full spectrum of lung cancer etiology from smoking initiation, smoking dependency to lung cancer development and outcome. It combines a traditional molecular epidemiology design with more integrative approaches by examining epidemiological, molecular, and clinical data together. To comprehensively investigate the effect of tobacco smoking behaviors on genomic or epigenomic alterations, we performed a multi-omics study including whole-genomic, transcriptomic, and epigenomic profiles in a total of 221 individuals from the EAGLE study.

  Study phs002992

• Transcriptomic profiling of fragile X syndrome unmethylated full mutation carriers

  Total RNA sequencing of fibroblasts from two unrelated FMR1 unmethylated full mutation carriers, a fragile X patient and a control individual. The existence of rare, unmethylated full mutation carriers who carry the mutation that causes fragile X syndrome but do not gain methylation at the locus offers a rare opportunity to study the mechanisms underlying fragile X syndrome. This study aims to compare the transcriptomes of these four individuals in order to elucidate the mechanism behind the methylation a the FMR1 CGG repeat expansion that causes Fragile X syndrome.

  Study EGAS50000000647

• Gene expression data of 2D duodenum organoids with or without continuous flow

  We developed a monolayer culture system for small intestinal organoids, and then placed the culture plate on a rotator to generate a constant flow in the overlay medium. This mechanical stimulation facilitated the formation of villus-like structures from the monolayer of small intestinal organoids. We analyzed gene expression of 2D normal duodenum organoids with or without medium rotation. Total RNA was extracted from organoids with or without a four-day medium rotation, and after 0, 1, 2 or 4 days of medium rotation, and sequenced with HiSeq X Ten (Illumina).

  Study JGAS000256

• Optimized large-scale longitudinal biorepository of gastroesophageal adenocarcinoma patient-derived organoids

  To enable translation studies we created patient derived models to assess biomarkers, target validation, and patient response. To evaluate that the PDOs retain the genomic characteristics of the primary tumours we performed (WES) sequencing of 11 matched primary tumours and their matched organoid samples (total n=22). Libraries were sequenced using Illumina NovaSeq technology. Reads were aligned with BWA alignment to hg38. Files were processed following GATK best practices (version GATK 4.2.3.0). Variants were called using Mutect2. The dataset contains the alignmnent files (.bam) and the called mutations (.vcf).

  Study EGAS50000001614

• Single-nucleus RNA-seq of human fetal liver hematopoiesis

  The fetal liver is the primary haematopoietic organ during early human development, yet the timing and regulatory mechanisms governing blood formation remain incompletely understood. To define the cellular, transcriptional, and epigenetic changes underlying human fetal liver hematopoiesis over development, we generated a high-resolution, time-resolved single-nucleus multiome atlas of human fetal liver spanning 5–18 post-conception weeks (PCW) for CD45+CD235- cells. In total, 308,021 high-quality nuclei from 53 donors were profiled using paired chromatin accessibility and transcriptomic modalities. This study is for the gene expression.

  Study EGAS50000001631

• Single-nucleus ATAC-seq of human fetal liver hematopoiesis

  The fetal liver is the primary haematopoietic organ during early human development, yet the timing and regulatory mechanisms governing blood formation remain incompletely understood. To define the cellular, transcriptional, and epigenetic changes underlying human fetal liver hematopoiesis over development, we generated a high-resolution, time-resolved single-nucleus multiome atlas of human fetal liver spanning 5–18 post-conception weeks (PCW) for CD45+CD235- cells. In total, 308,021 high-quality nuclei from 53 donors were profiled using paired chromatin accessibility and transcriptomic modalities. This study is for the chromatin accessibility.

  Study EGAS50000001632

• Transcriptional effect of 4HTBZ on Caco-2 cells

  This study was performed to investigate the transcriptional effect of the H2S donor 4HTBZ on intestinal epithelial cells upon inflammatory stimulation. Caco-2/TC7 cells were pre-stimulated with interferon gamma (IFNG, 2.5 ng/mL) and tumor necrosis factor alpha (TNF, 10 ng/mL), followed by treatment with 4HTBZ (50 µM) or vehicle (0.1% DMSO) for 72 hours. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany), and cDNA libraries were prepared with the QuantSeq 3′ mRNA-Seq Kit (Lexogen, Inc.) and sequenced on an Illumina HiSeq4000 system.

  Study EGAS50000001237

• Acute_Lymphoblastic_Leukemia_Exome_sequencing_2_

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Acute Lymphoblastic Leukemia samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000200

• Acute_Lymphoblastic_Leukemia_Exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Acute Lymphoblastic Leukemia samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000201

• Myeloproliferative_Disorder_Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 myeloproliferative disorder samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000198

• Myeloproliferative_Disorder_Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 myeloproliferative disorder samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000199

• Acute_Lymphoblastic_Leukemia_Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Acute Lymphoblastic Leukemia samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000058

• RNA-seq data from 121 tumor 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). RNA-seq was performed using the QuantSeq kit FWD HT kit (Lexogen) using 500 ng input RNA from 121 tumor samples. Data provided here consist of 780 fastq files for RNA-seq.

  Study EGAS00001004505

• Genome-wide search to find the genetic elements underlying visual contour perception

  Contour integration is a key function of the visual system to deal with occlusion and discontinuity in natural scenes. The current study is the first one to investigate the genetic basis of this visual function in humans. A total of 2619 normal participants were tested on their ability to detect continuous contours embedded in a cluttered background with a standard psychophysical protocol. Multi-level genomic analysis was performed, involving heritability estimation based on single nucleotide polymorphism (SNP) and association testing at SNP and gene levels.

  Study EGAS00001003639

• Osteosarcoma mate-pair and RNA-sequencing

  DNA mate pair and RNA sequencing data of conventional osteosarcomas. Mate pair libraries, with average insert sizes of 2-4 kb, were prepared for sequencing using the Nextera Mate Pair Library Preparation Kit. Paired-end 76 base pair reads were generated using an Illumina NextSeq 500 sequencing instrument. Total RNA was enriched for polyadenylated RNA using magnetic oligo(dT) beads. Enriched RNA was prepared for sequencing using the TruSeq RNA Sample Preparation Kit v2 and paired-end 151 base pair reads were generated from the cDNA libraries using an Illumina NextSeq 500 instrument.

  Study EGAS00001003842

• 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.

  Study EGAS00001004507

• Gene expression profiling of nasopharyngeal carcinoma

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Study EGAS00001004542

• A transcriptome atlas of human skeletal muscles

  We generated a large transcriptome atlas of human skeletal muscles by collecting biopsies from 6 different muscles to determine molecular signatures that may be distinct between leg muscles. The biopsies were collected from gracilis (GR), semitendinosus (ST), vastus lateralis (VL), vastus medialis (VM), rectus femoris (RF), and gastrocnemius lateralis (GL) muscles. We also investigated molecular differences within the muscle by including two biopsies from the middle and distal sides of the semitendinosus muscle (STM and STD, respectively). In total, 128 samples from 20 individuals (aged 25 ± 3.6 yr) were analyzed.

  Study EGAS00001005904

• Multi-region whole-exome sequencing of 10 neuroblastoma cases

  To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region whole-exome sequencing on a total of 51 spatially separated tumor samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 1 relapsed neuroblastoma. We also assessed the impact of chemotherapy on the clonal expansion by sequencing tumour regions from one medium risk and one high-risk tumour for which we had matched samples obtained at diagnosis and after chemotherapy.

  Study EGAS00001004735

• Gene_regulation_of_human_CD4__Treg_cells_

  This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs). It includes whole genome sequence data for ChM-seq (118 H3K4me3, 118 H3K27ac and 6 inputs), ATAC-seq (114 samples) and whole transcriptome (141 samples). All individuals were genotyped (130 samples) using coreExome Illumina SNP chip array. The final quality filtered set included 123 individuals with RNA-seq data, 73 with ATAC-seq, 91 with H3K27ac ChM-seq and 88 with H3K4me3 ChM-seq data. A total of 62 individuals had QCed data for all the assays.

  Study EGAS00001003516

• UCSF Pediatric Bithalamic Glioma Genome Project

  Targeted next-generation sequencing of 13 pediatric bithalamic diffuse gliomas. BAM files of targeted next-generation DNA sequencing data of 13 pediatric gliomas, with multi-region sequencing data from 2 of these cases (17 total tumor samples). Genomic DNA was extracted from formalin-fixed, paraffin-embedded blocks of tumor tissue from using the QIAamp DNA FFPE Tissue Kit (Qiagen). Capture-based next-generation DNA sequencing was performed at the University of California, San Francisco Clinical Cancer Genomics Laboratory, using an assay that targets all coding exons of 480 cancer-related genes, select introns of 47 genes, and TERT promoter with a total sequencing footprint of 2.8 Mb (UCSF500 Cancer Panel). Sequencing libraries were prepared from genomic DNA, and target enrichment was performed by hybrid capture using a custom oligonucleotide library (Nimblegen SeqCap EZ Choice). Captured libraries were sequenced as paired-end 100 bp reads on an Illumina HiSeq 2500 instrument. Duplicate sequencing reads were removed computationally to allow for accurate allele frequency determination and copy number calling.

  Dataset EGAD00001005499

• FASTQ files of the polyA+ (oligo-dT) RNA-Seq dataset from the POPS SGA (Small for Gestational Age) samples and their matched controls.

  FASTQ files of the polyA+ (oligo-dT) RNA-Seq dataset from the POPS SGA (Small for Gestational Age) samples and their matched controls. The POP study placental biopsies were collected within 30 minutes of birth and flash frozen in RNAlater (ThermoFisher). For each biopsy, total placental RNA was extracted from approximately 5 mg of tissue using the “mirVana miRNA Isolation Kit” (Ambion) followed by DNase treatment (“DNA-free DNA Removal Kit”, Ambion). RNA quality was assessed with the Agilent Bioanalyzer and all the samples with RIN values ≥ 7.0 were used in the downstream experiments. RNA-libraries were prepared from 1g of total placental RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina) which captures polyA-tailed transcripts by oligo-dT beads, then pooled and sequenced (single-end, 50bp) using a Single End V4 cluster kit and Illumina HiSeq2500

  Dataset EGAD00001006304

• Analyzing the expression profiles of genes in ureters with and without indwelling stents using RNAseq 

  The objective of the work is to explore the pathways and mechanisms driving inflammation and fibrosis in stented ureters. In total, 6 pigs underwent cystoscopic unilateral ureteral stent insertion for 14 days. Ureteral tissue was harvested in 3 pigs, while the remaining 3 pigs had their stents removed, and were recovered for 7 days. Three separate pigs served as controls. Stents cause significant inflammation and fibrosis of ureters. Gene set enrichment analysis confirmed fibrotic changes and tissue proliferation and suggests that epithelial-mesenchymal transition is a driver of fibrosis.

  Study EGAS00001006855

• Dataset Rdata segmentations

  This data set contains an .Rdata file for all the processed segmentation profiles from 81 lpWGS samples included used in downstream analyses from Github repository Evo_history_CACRC. Lastly, there is an .Rdata object with 50 segmentations for 50 total samples from 25 sporadic SNP adenomas used in the comparison with colitis samples.

  Dataset EGAD00010001586

• Whole-exome sequencing and microRNA profiling predicted relapse risk of stage I lung adenocarcinomas for the study and all the datasets.

  This dataset contains CEL files and rma normalized expression value for microarray of stage I lung adenocarcinomas from Asian patients. In total, there are 69 patients and 138 samples, including 69 tumor samples and 69 adjacent normal samples.

  Dataset EGAD00010001901

• Oxford Nanopore WGS

  A total of 20 individuals, were analyzed using Oxford Nanopore Technologies long-read sequencing. Each individual was sequenced on one PromethION flow-cell, providing approximately 25-30X coverage of the genome. The data is deposited as nanopore BAM files with methylation information included.

  Dataset EGAD50000000573

• GBM Study Complete Raw Data

  Tumors from 173 GBM patients were analysed for somatic mutations to generate a personalized peptide vaccine targeting tumor-specific neoantigens. Exome libraries for 173 glioblastoma tumors and matched normal DNA were sequenced on Illumina platform, alongside total RNA from the tumors.

  Dataset EGAD50000000650

• Genomic WES plasma control samples

  This datasets consists os genomic WES of paired-end raw data (FASTQ R1, R2 and UMI sequence) obtained from plasma and HapMap control samples. Specifically, it consists in two Hapmap samples (NA12877, NA12878) and 2 plasma standarts (HD780 and HD816) with VAF mutations at 0.0%, 0.1%, 1.0%, and 5.0%, in total 21 plasma samples.

  Dataset EGAD50000000805

• LRS - episignature samples

  This dataset contains 22 long-read WGS fastq.gz files sequenced ONT PromethION. In total the dataset includes 20 individuals, for all of them sequencing starting from blood was performed, and for one of the samples sequencing from urine and from the buccal swab was also included. In all the samples methylation calls are included in the fastq file.

  Dataset EGAD50000001000

• Whole exome sequencing of ETV::RUNX1 positive acute lymphoblastic leukemia

  This dataset contains whole exome sequencing of ETV::RUNX1 positive acute lymphoblastic leukemia. Germline and leukemia samples were sequenced in pairs. A total of 94 samples were sequenced and reads were aligned to hg19 genome reference. Aligned bam files are provided in this data set.

  Dataset EGAD50000001184

• CHIP panel sequencing of rheumatoid arthritis patients

  Targeted NGS sequencing data (bam and index files aligned to hg38) a total of 573 newly diagnosed, untreated RA patients and 163 healthy controls. The sequencing panel included 65 genes recurrently mutated in myeloid malignancies, to capture clonal hematopoiesis of indeterminate potential (CHIP) mutations. The median target coverage was 1700x across samples.

  Dataset EGAD50000001300

• Mechanism of Decitabine response in MDS/AML patients

  The dataset includes single cell RNA sequencing data from 17 AML/MDS patients undergoing a decitabine clinical trial. In total 47 samples were interrogated using 10X genomics ChromiumTM 140 Single Cell 5' Reagent Kit. The dataset includes bam files for each sample generated using CellRanger with default parameters.

  Dataset EGAD50000001354

• Whole genome sequencing of patient derived cancer and normal organoids

  The dataset includes whole genome sequencing data generated from regional patient derived colorectal cancer (CRC) and adjacent normal tissue organoids. The dataset contains samples from a total of 10 different early CRC biobank patients from 2 different sequencing runs.

  Dataset EGAD50000002204

• Deep multi-region WGS of lung cancer tumours

  Deep WGS (germline and 2-5 tumour regions) was performed on 20 patients: 13 lung adenocarcinoma, 5 squamous cell carcinoma, 2 small-cell lung cancers. A total of 68 BAM files are provided, where tumours were sequenced to 60x or 150x depth.

  Dataset EGAD00001005287

• WGS of human colorectal cancer organoid exposed to genotoxic pks+ E. coli

  Organoid cultures were exposed to two different E.Coli strains and a dye control with three biological duplicates. Their original culture was harvested as a control. In total 10 organoid cultures were whole-genome sequenced using the Novaseq6000 platforms. The data is deposited as .bam format.

  Dataset EGAD00001005416

• Transcriptomic profiling of RIRCD patient skeletal muscle, comparing recovered to affected disease phase.

  Illumina MiSeq total RNA sequencing profiles of skeletal muscle biopsies from patient F3/1M during affected disease phase (4 replicates: F3-1M_Affected_1, F3-1M_Affected_2, F3-1M_Affected_3, F3-1M_Affected_4) compared to recovered phase (F3-1M_Recovered_1, F3-1M_Recovered_2, F3-1M_Recovered_3, F3-1M_Recovered_4).

  Dataset EGAD00001006382