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• WGS data of paediatric ETV6::RUNX1 B cell acute lymphoblastic leukemia (set3)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of two ETV6::RUNX1 ALL patients (ALLT-397, ALLK-132). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeqX Plus.

  Dataset EGAD50000002287

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of five B-other ALL patients (ALLT-327, ALLT-334, ALLT-357, ALLK-108, ALLT-361). Sequencing library was made using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000002157

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of four B-other ALL patients (ALLT-321, ALLT-311, ALLT-314, ALLT-319). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using TruSeq DNA PCRfree library preparation kit v1. Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000002156

• Phenotype, genotype, and transcriptome data from three South Eastern Bantu groups in the SABR study

  Phenotypic data, whole genome sequencing, blood RNA-seq, imputed variant calls, cell type estimates, gene expression levels, splicing measurements, and analysis covariates from South African Blood Regulatory (SABR) resource participants, which includes South Eastern Bantu-speaking groups.

  Dataset EGAD50000001477

• scRNA-seq and scATAC-seq data of human cardiac fibroblasts

  6 scRNA-seq and 4 scATAC-seq datasets on cardiac fibroblasts derived from two patients (P1, P2). The sequencing dataset consists of two control samples pretreated with vehicle (resting, only scRNA-seq data available); two samples stimulated with TGFb; and two samples pre-treated with KAT5 inhibitor, followed by stimulation with TGFb (iKAT5).

  Dataset EGAD50000001224

• Genomic and Transcriptomic Data in GBM Patients Undergoing anti-PDL1 Therapy

  This dataset comprises whole exome sequencing data from 29 tumor-normal pairs and RNA-seq data from 39 tumors of newly diagnosed IDH-wt GBM patients. It includes analyses such as variant calls, copy number variations, the transcriptomic expression matrix, and patient metadata and outcomes.

  Dataset EGAD50000001154

• Metagenomic characterization of tracheal aspirates from non-pulmonary sepsis patients

  Metagenomic characterization of tracheal aspirates from non-pulmonary sepsis patients. This dataset consists of non-human read data from shotgun sequencing in sepsis case samples from lung aspirates. The dataset consist of 32 paired FASTQ files sequenced in paired-read mode 2x150 bp using an Illumina HiSeq 4000 sequencer.

  Dataset EGAD50000000561

• Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation

  Raw sequencing files from scRNA-seq dataset used in Schmassmann et al. 2023. Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation. Elife 12 (https://elifesciences.org/articles/92678) Dataset content: 14 samples from 5 donors File type: paired-end fastq files Technology: Illumina sequencing Experimentation used: scRNA-seq using the 10X technology

  Dataset EGAD50000000434

• Genome and transcriptome sequence data from a rectal adenocarcinoma patient

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

  Dataset EGAD00001011040

• Genome and transcriptome sequence data from a thymoma patient

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

  Dataset EGAD00001011039

• Paired RNA seq of wild type VDH15 cells (3 replicates) - a cell line of oral squamous cell carcinoma (OSCC)

  Paired RNA seq of wild type VDH15 cells (3 replicates) - a cell line of oral squamous cell carcinoma (OSCC). RNA was extracted and sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocol. The sequencing was done using Illumina Novaseq 6000.

  Dataset EGAD00001010172

• BCSA_Exome+SmartSeq3

  Multiple regions were cut out of each tumor extracted form breast cancer patients and two experiments were run: - Whole exome sequencing on each of the regions plus an adjacent normal tissue sample - Smart-Seq3 Single cell RNA sequencing on EPCAM+ CD45- sorted cells from different tumor regions

  Dataset EGAD00001009781

• RNA-seq of T-ALL patient-derived xenograft (PDX) samples

  This dataset includes 4 samples profiled by high-throughput Illumina sequencing, in bam format, aligned to GRCh37. Human patient T-ALL samples were serially propagated as xenografts in immunodeficient mice. The samples were collected after development of frank leukemia in recipient mice.

  Dataset EGAD00001009749

• Dataset GBM 2022

  The cellular origin and differentiation status of glioblastoma by scRNA-seq

  Dataset EGAD00001008745

• Human and rat skeletal muscle multiomic profiling sequencing data

  Illumina sequencing data (fastq files) representing single-nucleus (sn) ATAC-seq, snRNA-seq, bulk ATAC-seq, and snATACseq+snRNAseq multiomics data from human and rat skeletal muscle samples (19 libraries total). Includes a README file that describes the relationship between libraries, samples, and files.

  Dataset EGAD00001008323

• Transcriptome Changes in ASD (NRXN1α+/-) iPSC-derived neurons

  This dataset contains 10 fastq files from 10 cell lines (4 cell lines from 3 patients and 6 cell lines from 4 controls) that have undergone 50bp single end sequencing with PolyA enrichment strategy (BGI project number HUMpcsN). *please note one of the samples (Patient_4) was named in error and should be corrected to Patient_3 during analysis

  Dataset EGAD00001007993

• single cell transcriptome data of gluten-specific T cells

  The data contains paired-end fastq files of 1440 single cells transcriptome sequencing data from 4 Celiac disease patients. CD4+ T cells were sorted by HLA-DQ-gluten tetramers carrying four immunodominant gluten epitopes. All single cell libraries were constructed following SmartSeq2 and sequenced on Illumina NextSeq 500.

  Dataset EGAD00001007975

• The evolution of hematopoietic cells under cancer therapy

  WGS TAML samples with their remission controls obtained from bone marrow.

  Dataset EGAD00001007706

• The natural history of clonal haematopoiesis: colony WGS

  Whole-genome sequencing of 288 single-cell-derived blood colonies from 3 elderly individuals with clonal haematopoiesis.

  Dataset EGAD00001007684

• iAMP21 RNAseq data set

  RNAseq samples from the iAMP21 study

  Dataset EGAD00001007577

• V(D)J and 5' Gene Expression data on patients with aplastic anemia

  Chromium V(D)J and 5' Gene Expression platform (10X Genomics) was used to study patients with aplastic anemia. CD45+ cells from two patients (patient AA-3: 3 longitudinal samples from bone marrow and patient AA-4: 3 longitudinal samples from peripheral blood) were analysed. The raw data was processed using Cell Ranger 3.0.1 pipelines.

  Dataset EGAD00001006937

• Skeletal muscle transcriptomic comparison between long-term trained and untrained men and women

  We generated global skeletal muscle transcriptomic data from long-term endurance (9 men, 9 women) and strength (7 men) trained individuals. These data were compared with healthy age-matched untrained controls (7 men, 8 women). All 40 samples were then multiplexed in 1 lane and sequenced (2x50bp paired end) on the Illumina NovaSeq 6000.

  Dataset EGAD00001006067

• Next Generation Sequencing Characterization of Tregs in Human Peripheral Blood during Autoimmunity

  Tregs were sorted as CD4+CD25+CD127- cells from peripheral blood of 14 healthy individuals, 8 patients with systemic lupus erythematosus, 9 patients with rheumatoid arthritis, and 11 patients with multiple sclerosis. RNA was extracted and polyA libraries were prepared using the Illumina Truseq sample preparation kit v.2. Single-end sequencing was performed on NextSeq500.

  Dataset EGAD00001006193

• Whole Exome Sequencing of Spanish Patients diagnosed with rare ophtalmogenetic disorders.

  Whole Exome sequencing of a set of Spanish patients suffering rare genetic diseases. The set consists of 4 patients, one was diagnosed with Retinitis Pigmentosa (RP-1629), another one was diagnosed with Macular Dystrophy (MD-0235) and two were diagnosed with Leber's Congenital Amaurosis (LCA-0081 and LCA-0103).

  Dataset EGAD00001005746

• Hepatitis B Viral sequence reads

  Deep sequencing of viral samples (average ~9,000x coverage) from patients chronically infected with Hepatitis B (HBV). Whole HBV genome sequencing of 1467 patients (1102 in discovery and 365 in validation cohort) chronically infected with HBV at baseline. The patient population contained HBV genotypes A (98), B (285), C (716), D (356), E (7), and F (5) with 977 HBeAg-positive and 490 HBeAg-negative patients.

  Dataset EGAD00001005075

• single-cell transcriptomics data from immune cells

  Smart-seq2 protocol was used to perform single cell RNA-sequencing on 465 immune cells. The immune cells analysed include 215 HLA-DQ2: gluten-(DQ2.5-glia-α1, -α2, -ω1, and -ω2) tetramer-sorted T cells, 247 transglutaminase 2 (TG2)-positive plasma cells from intestinal biopsy or peripheral blood from celiac disease patients, and 3 unassigned cells in 3 batches.

  Dataset EGAD00001004081

• ChIP sequencing data to study therapeutic targeting of ependymoma

  This dataset contains ChIP sequencing data from 24 patients. ChIP of 5–10 mg flash-frozen primary ependymoma tumour was performed using 5 mg H3K27ac antibody per ChIP experiment. The enriched DNA has been sequenced on a Illumina HiSeq2000 instrument in paired-end mode. Up to two lanes per sample have been sequenced resulting in 70 Fastq files.

  Dataset EGAD00001003979

• A novel subset of human CD33+ haematopoietic stem cells characterized at single-cell resolution

  This dataset comprises single-cell RNA sequencing of the human Lin-CD34+38-45RA-90+49f+ phenotype isolated from 2 normal cord donors. Library preparation was performed following a modified CEL-Seq2 protocol.

  Dataset EGAD00001003955

• Whole genome sequencing data of tumor/normal pairs from 20 patients with hepatoblastoma

  This dataset provides whole genome sequencing data of tumor/normal pairs from 20 patients with hepatoblastoma using the illumina Novaseq sequencing system. It includes 40 samples (20 normals and 20 hepatoblastoma tumors). Our comprehensive analysis identified somatic mutations, structural variations, copy number variations and non-coding variants in hepatoblastoma.

  Dataset EGAD00001003914

• APCDR AGV Project: Low coverage (4x-8x) sequence data from 3 African populations (VCFs)

  Low coverage (4x-8x) Illumina HiSeq curated sequence data from 3 African populations from the AGV project; 100 Baganda from Uganda (4x), 100 Zulu from South Africa (4x), and 120 Gumuz, Wolayta, Oromo, Somali and Amhara from Ethiopia (8x). Pre-processed, jointly called and filtered with GATK, refined with Beagle3, phased with SHAPEIT2.

  Dataset EGAD00001001663

• DKFZ-HIPO Data Access Committee of Heidelberg Center for Personalized Oncology

  Dac EGAC00001000452

• CBD-RAW-SC-GEX: 10X Single-Cell Gene Expression

  Raw Illumina sequencing data and CellRanger BAM output files. For further information regarding this dataset, please contact Stephen Sansom at contact@combat.ox.ac.uk.

  Dataset EGAD00001008007

• ICGC PCAWG Dataset: LAML-KR_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LAML-KR.

  Dataset EGAD00001002119

• ICGC PCAWG Dataset: BTCA-SG_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BTCA-SG.

  Dataset EGAD00001002121

• ICGC PCAWG Dataset: BRCA-UK_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BRCA-UK.

  Dataset EGAD00001002122

• ICGC PCAWG Dataset: MALY-DE_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MALY-DE.

  Dataset EGAD00001002123

• ICGC PCAWG Dataset: EOPC-DE_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: EOPC-DE.

  Dataset EGAD00001002124

• ICGC PCAWG Dataset: BOCA-UK_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BOCA-UK.

  Dataset EGAD00001002125

• ICGC PCAWG Dataset: PRAD-UK_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PRAD-UK.

  Dataset EGAD00001002126

• ICGC PCAWG Dataset: PBCA-DE_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PBCA-DE.

  Dataset EGAD00001002127

• ICGC PCAWG Dataset: PRAD-CA_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PRAD-CA.

  Dataset EGAD00001002128

• ICGC PCAWG Dataset: BRCA-EU_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BRCA-EU.

  Dataset EGAD00001002129

• ICGC PCAWG Dataset: CLLE-ES_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: CLLE-ES.

  Dataset EGAD00001002130

• ICGC PCAWG Dataset: RECA-EU_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: RECA-EU.

  Dataset EGAD00001002131

• ICGC PCAWG Dataset: PACA-AU_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PACA-AU.

  Dataset EGAD00001002132

• ICGC PCAWG Dataset: PAEN-AU_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PAEN-AU.

  Dataset EGAD00001002154

• ICGC PCAWG Dataset: PAEN-IT_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PAEN-IT.

  Dataset EGAD00001002153

• ICGC PCAWG Dataset: LIRI-JP_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LIRI-JP.

  Dataset EGAD00001002155

• ICGC PCAWG Dataset: ESAD-UK_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ESAD-UK.

  Dataset EGAD00001002156

• ICGC PCAWG Dataset: MELA-AU_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: MELA-AU.

  Dataset EGAD00001002157

• Clonal fitness inferred from timeseries modeling of single cell cancer genomes

  Progress in defining genomic fitness landscapes in cancer by copy number alterations (CNA) has been impeded by lack of single cell and timeseries sampling. We generated 42,000 single cell whole genomes (scWGS) from breast epithelium and primary triple negative breast cancer (TNBC) patient-derived xenografts (PDX) collected during multi-year time series. Using a Wright-Fisher population genetics model, we inferred reproducible CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy, with accurate forecasting of experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDX resulted in cisplatin resistant clones that had shown low fitness in the untreated setting. By contrast high fitness clones from treatment naive controls were eradicated reflecting an inversion of the fitness landscape. Upon drug release selective pressure dynamics were reversed indicating a fitness cost of treatment resistance. Taken together, our findings reveal clonal fitness dynamics linked to CNA and therapeutic resistance in polyclonal tumours.

  Study EGAS00001004448

• IGH repertoire sequencing of GZMB+ and GZMB− B cells

  This dataset contains high-throughput sequencing data of immunoglobulin heavy chain (IGH) repertoires from sorted GZMB⁺ and GZMB⁻ B cell subsets. Samples were obtained from healthy donors (Healthy Volunteers, HVs) and drug-free tolerant kidney transplant recipients (TOLs). Libraries were generated from genomic DNA using targeted BIOMED-2 PCR amplification and sequenced on an Illumina MiSeq platform. The dataset enables comparative analysis of B cell clonality, diversity, and somatic hypermutation patterns.

  Dataset EGAD50000002452

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set5)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of four hyperdiploid ALL patients (ALLT-502, ALLK-130, ALLK-137, ALLK-139). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq X Plus.

  Dataset EGAD50000002428

• Transcriptome analysis of human muscle/myofibers carrying the human nemaline myopathy type 6-associated KBTBD13-R408C variant.

  This dataset contains mRNA-seq results from eleven samples from human donors, each sample being composed of 5-10 rebulked fiber type-specific myofibers. This sample set includes; 1) Three FT-I and three FT-IIa rebulked samples from control individuals 2) Three FT-I and two FT-IIa rebulked samples from NEM6 patients with a KBTBD13R408C variant (NP_001094832.1: p.Arg408Cys)

  Dataset EGAD50000002408

• Spatial CosMx Human 6K

  we profiled the cellular composition and TME spatial organization in 4 ICB-resistant HCC patients using single-cell spatial transcriptomics (CosMx Human 6K Discovery Panel). We identified 397 fields-of-view (0.51 mm by 0.51 mm) of hematoxylin and eosin (H&E)-defined tumor and stromal regions followed by cell segmentation using a nuclear stain plus 4 protein markers, yielding 485,209 high-confidence single-cell profiles that were subsequently categorized into distinct cell types based on marker gene annotation.

  Dataset EGAD50000002052

• WES_dataset1

  Fourteen MEITLs and one EATL previously had been sequenced using the SureSelectXT Target Enrichment System (Agilent Technologies, Santa Clara, CA, USA).

  Dataset EGAD50000001620

• Human Single-Oocyte Transcriptome - Control and Cannabis Treated

  RNAseq data of human single oocytes exposed to THC and its metabolites, (mean concentration measured in the follicular fluid, THC1, n=95, 25 ng/mL Δ9-THC, 5 ng/mL 11-OH-THC, 50 ng/mL 11-COOH-THC) or a supraphysiologic, THC2, n=93, 100 ng/mL Δ9-THC, 50 ng/mL 11-OH-THC, 200 ng/mL 11-COOH-THC).

  Dataset EGAD50000001534

• mUM patient biopsies bulk RNAseq

  Tumour biopsies were obtained from uveal melanoma patients (n = 35) pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system

  Dataset EGAD50000001225

• WES of head and neck cancer patients refractory to anti-PD-1 therapy

  Whole exome sequencing (WES) was performed on baseline (before low-dose 5-aza treatment) blood and tumor paired samples from 12 participants with head and neck cancer who were refractory to anti-PD-1 therapy. DNA extractions were performed by the Broad Institute of MIT and Harvard using Qiagen AllPrep DNA/RNA kits (Cat. 80204). In total, 24 150-bp pair-end WES data were generated by Illumina.

  Dataset EGAD50000001011

• Whole-genome cfDNA TAPS sequencing data from 91 people with various types of cancer and from non-cancer controls

  TAPS data in the form of BAM files from 214 samples: plasma (at 80x) and matched germline (at 30x) pairs from 61 cancer and 30 non-cancer subjects, fresh-frozen matched tumour biopsies (at 80x) from 16 subjects, as well as several follow-up plasma samples (at 80x) from 10 subjects with colorectal cancer.

  Dataset EGAD50000000996

• Targeted capture sequencing to identify MYC, BCL2, and BCL6 rearrangements in non-Hodgkin lymphoma

  Targeted capture sequencing of 364 samples representing a mix of Burkitt lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, and high-grade B-cell lymphomas with MYC and BCL2 or BCL6 rearrangements. Capture space covers 3.5 Mb of the human genome including regions around MYC, BCL2, BCL6, PAX5, and IGH/K/L.

  Dataset EGAD50000000489

• Comparison clinical recommendation MASTER and panel sequencing: Genomic data

  This dataset contains 29 case/control samples of WES and WGS sequencing data. Sequencing was performed on Illumina HiSeq X using TruSeq Stranded DNA Kit. The sequencing was always paired.

  Dataset EGAD50000000624

• RNA-seq dataset

  RNA-seq data from CD20+ sorted cells obtained from peripheral blood and lymph node Follicular Lymphoma patients. These samples were unstimulated after thawing and additionally, peripheral blood samples were stimulated during 7 days in culture as described in Dobaño-López C et al. Stranded RNA-seq libraries were performed using the TruSeq library kit (Illumina, San Diego, CA, USA). Libraries were sequenced on a NextSeq 2000 (Illumina) in a 2x50bp length.

  Dataset EGAD50000000347

• RNA sequencing of BCP-LBL patients samples

  In order to perform comprehensive transcriptomics and gene fusion analyses of a cohort of BCP-LBL patients, we performed RNA sequencing of 49 tissue samples from BCP-LBL 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 EGAD50000000419

• bfast CohortD ctDNA manifest

  A list of ctDNA samples included in the dataset.

  Dataset EGAD50000000146

• Single-cell analysis of matched FFPE and frozen tissue samples reveals comparable resolution of intratumoural heterogeneity

  Testing the differences between FFPE and fresh frozen derived single cell results.

  Dataset EGAD00001015781

• Genome and transcriptome sequence data from a malignant peripheral nerve sheath tumor patient

  Genome and transcriptome sequence data from a malignant peripheral nerve sheath tumor patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015583

• Single-cell RNA and TCR sequencing of 37 PBMC pools of advanced HCC patients.

  scRNAseq and scTCRseq of serial peripheral blood mononuclear cell (PBMC) samples (n=72) taken at various timepoints before and during treatment (Week 0 (W0), Week 3 (W3), Week 6 (W6)). PBMC samples were pooled together into 37 pools, loading 2 or three samples per lane in the 10X Genomics chip, in equal proportions, according to a pre-designed pooling matrix.

  Dataset EGAD00001011345

• ATAC-seq and RNA-seq datasets of CD14+ monocytes from healthy donors

  This dataset consists of functional genomic data from 6 healthy donors taken from CD14+ monocytes upon different immune stimulations. It contains 150 paired end fastq files consisting of 30 total RNA-seq samples across 4 runs and 30 ATAC-seq samples. The samples were sequenced on Illumina HiSeq4000 platform.

  Dataset EGAD00001011113

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001010315

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

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

  Dataset EGAD00001010318

• Whole Genome Sequencing of Head and Neck Angiosarcoma

  This dataset contains 55 Whole Genome Sequencing of the study titled Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma.

  Dataset EGAD00001010140

• NEC

  This multi-centre, non-randomized, open-label, phase II trial (NCT03016338), assessed niraparib monotherapy (cohort 1, C1), or niraparib and dostarlimab (cohort 2, C2) in patients with recurrent serous or endometrioid endometrial carcinoma. The primary endpoint was clinical benefit rate (CBR). Secondary outcomes were safety and objective response rate (ORR). Translational research was an exploratory outcome. Potential biomarkers were evaluated in archival tissue by immunohistochemistry and next generation sequencing panel. Feasibility of liquid biopsy by ctDNA was assessed.

  Dataset EGAD00001010056

• Prostate cancer m6A epitranscriptome

  Using meRIP-sequencing, we profiled N-6 methyladenosine (m6A) in a cohort of 148 primary prostate cancer samples as part of the Canadian Prostate Cancer Genome Network project (CPC-GENE). Paired-end sequencing of 150 bp reads were mapped to GRCh38.p13 using annotations from gencode.v34.chr_patch_hapl_scaff.annotation.gtf. Peaks were called using MeTPeak, joint peaks were identified and IP reads were quantitated, normalized and adjusted using Input reads to obtain estimates of m6A abundance.

  Dataset EGAD00001009869

• Single-cell RNA-seq of patient-derived organoids across three generations

  Single-cell RNA-seq of first-, second-, and third-generation patient-derived organoids. Obtained using the 10X Genomics single-cell 3' expression solution (v3 chemistry). First- and second-generation PDOs from one patient and first-, second-, and third-generation PDOs from three additional patients.

  Dataset EGAD00001008431

• Stage-specific gene and transcript dynamics in human male germ cells

  To study global transcriptional dynamics during human spermatogenesis we sequenced total RNA of human testicular biopsies with 5 specific histological phenotypes: Sertoli cell-only (SCO, n=3), spermatogenic arrests at the spermatogonial (SPG, n=4), spermatocyte (SPC, n=3), and spermatid (SPD, n=3) level, as well as normal spermatogenesis (Normal, n=3).

  Dataset EGAD00001008652

• Targeted seqencing of serrated lesions of the colorectum

  Dataset consists of Oncomine Comprehensive Cancer Panel v3 sequencing of 16 tumor-normal mucosa pairs. Tumors include 8 sessile serrated lesions (SSL), 3 sessile serrated lesions with dysplasia (SSL/D), 2 traditional serrated adenomas (TSA) and 3 tubular adenoma s(TA).

  Dataset EGAD00001008191

• Single-nucleus Isoforms of Down Syndrome Brains (long-read)

  16 DS and Control brains samples were prepared using the 10X Genomics Single Cell 3' v3 kit. Pre-fragmented cDNA libraries were loaded onto a Pacific Biosciences Sequel II to sequence single-nucleus isoforms.

  Dataset EGAD00001008286

• Genome and transcriptome sequence data from an unspecified tissue chordoma patient

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

  Dataset EGAD00001008013

• NGS reads files of PSCCE

  The aligned bam file of next generation sequencing performed on PSCCE.

  Dataset EGAD00001007002

• Summary statistics of meta-analysis using two genome-wide association study of inflammatory bowel disease in Koreans.

  We combined samples from 1,469 inflammatory bowel disease (IBD) patients consisted of 896 Crohn’s disease (CD) and 573 ulcerative colitis (UC) and 4,041 controls used in our previously published GWAS with 1,726 additional IBD patients (725 CD and 1,001 UC) and 378 additional controls genotyped using the Asian Screening Array (ASA). We uploaded summary statistics of three meta-analyses in text files.

  Dataset EGAD00001006983

• Whole genome sequencing of HSPCs and pAML

  Whole genome sequencing data (Illumina HiSeq and NovaSeq) of clonal cultures derived from pediatric human bone marrow-derived hematopoietic stem and multipotent progenitor cells (in total 44 samples from 10 donors) and bulk pediatric acute myeloid leukemia blasts (in total 6 samples from 6 patients) to study the mutation accumulation.

  Dataset EGAD00001006338

• AT-AML samples dataset

  Serial samples from one AT-AML patient as described in publication Goldgraben et al Pediatric Blood & Cancer 2020. Whole exome sequencing of a AT-'germline' blood sample, one bone marrow sample (at AML diagnosis) and 3 AML blood samples. Library preped using the Illumina Nextera Rapid Capture Exome Enrichment Kit, and sequenced as PE150 on HiSeq4000. Provided: 5 BAM files (GRCh37); 2 VCF analyses (germline and somatic)

  Dataset EGAD00001006090

• European Roma whole genomes sequences

  Pair end fastq file of 40 Roma whole genome sequence data. This dataset contains the fastq files obtained using illumina hiseq X generated reads, ~30X coverage. 10 Makedonian Roma - Balkan Roma 10 Spanish Roma - North/Western Roma 10 Hungarian Roma - Vlax and Romungro Roma 5 Lithuanian Roma - North/Western Roma 5 Ukranian Roma - Romungro Roma.

  Dataset EGAD00001006024

• Genome and transcriptome sequence data from a metastatic rectal carcinoma patient

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

  Dataset EGAD00001005825

• Genome and transcriptome sequence data from an uveal melanoma patient

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

  Dataset EGAD00001005824

• Genome and transcriptome sequence data from a breast ductal carcinoma patient

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

  Dataset EGAD00001005823

• Genome and transcriptome sequence data from a pancreatic cancer patient

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

  Dataset EGAD00001005762

• Genome and transcriptome sequence data from a metastatic pancreatic neuroendocrine patient

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

  Dataset EGAD00001005763

• BulkTCR-sequencing data from different human intestinal CD8 T cell subsets.

  5000 cells of each subset of CD8 T cells (CD103-KLRG1+, CD103-KLRG1- and CD103+ from LP and CD103+ IELs) were sorted into tubes. A modified SMART protocol was used in first-strand cDNA synthesis, and TCRalpha / TCRbeta genes were amplified in two rounds of semi-nested PCR reaction, following the method described in detail in Risnes et al., 2018.

  Dataset EGAD00001005049

• Genome and transcriptome sequence data from a metastatic rectal carcinoma patient

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

  Dataset EGAD00001004898

• Genome and transcriptome sequence data from a locally advanced breast cancer patient

  Genome and transcriptome sequence data from a locally advanced breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004897

• Whole exome sequencing and target gene sequencing of ESCC cases and healthy controls from Henan high-risk region

  In total, 186 FH+ ESCC cases were sequenced using whole-exome sequencing, then 1935 ESCC cases and 1186 geographically-matched healthy controls were sequenced using 7 Mb custom designed Roche SeqCap kit which targeted about 600 genes. The libraries were constructed and then sequenced in Illumina platform.

  Dataset EGAD00001004556

• WES analysis in identifying additive genetic factors that may contribute to the occurrence of moyamoya in neurofibromatosis type 1

  Five subjects from pedigree with co-occurrence of neurofibromatosis type 1 and moyamoya were sequenced in duplicate (0 and1). Kinship and phenotype: NF025, NF026 and NF027 were sibling all affected by neurofibromatosis type 1. NF026 also presented moyamoya. NF0262 and NF0263 were sibling both affected by neurofibromatosis type 1. NF0262 also presented moyamoya. NF026 and NF0262 were first cousins.

  Dataset EGAD00001004157

• The spatio-temporal evolution of lymph node spread in early breast cancer

  Set of multi-region sequenced breast cancer primary samples, lymph nodes and ctDNA. We collected samples from 11 breast cancer patients with lymph node involvement but no sign of distant metastasis. We performed a mix of whole-exome sequencing, targeted capture sequencing, and whole-genome sequencing of primary tumour samples and lymph nodes, as well as targeted capture sequencing of circulating tumour DNA.

  Dataset EGAD00001004122

• Bulk RNASeq on CD8+CD69+CD103+ and CD8+CD69+CD103- T cells form breast cancer.

  CD8+CD69+CD103+ and CD8+CD69+CD103- T cells were flow sorted from 1 primary triple negative breast cancer, 1 primary HER2 amplified breast cancer, and 1 triple negative liver metastasis. Prior to flow sorting, fresh tumor samples were digested to produce single cell homogenates on the day of surgery. Following RNA extraction, RNASeq was performed using polyA selection.

  Dataset EGAD00001003964

• GnRH Agonist-Induced Ovarian Suppression and Ovarian Steroids in PMDD and Controls

  In this study, lymphoblastoid cell line cultures (LCLs) from women with premenstrual dysphoric disorder (PMDD) and asymptomatic controls were compared via whole-transcriptome sequencing (RNA-seq) during untreated (ovarian steroid-free) conditions and after estradiol and progesterone treatment. In untreated LCLs, pathway analysis of the LCL transcriptome revealed, among others, over-expression of ESC/E(Z) complex genes (an ovarian steroid-regulated gene silencing complex) with significant overexpression of MTF2, PHF19, and SIRT1 (P<0.05) in cells from women with PMDD compared with controls. Finally, mRNA expression of several ESC/E(Z) complex genes were increased by progesterone in controls only, and decreased by estradiol in PMDD LCLs.

  Study phs001344

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set3)

  The dataset includes FASTQ and BAM/CRAM files from diagnostic and matched remission (control) samples of eight hyperdiploid ALL patients (ALLT-364, ALLT-367, ALLT-368, ALLT-371, ALLT-377, ALLK-111, ALLT-382, ALLT-395). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), NEBNext® Ultra™ II DNA Library Prep Kit (Cat No. E7645). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002427

• Oxford Nanopore Adaptive Sampling WGS

  Eight samples were analyzed on an Oxford Nanopore MinION flow-cell, and to evaluate multiplexing, four samples were run together on one flow-cell on the P2 Solo device. Using adaptive sampling, we targeted 10 regions of different structural variant types, including deletions, translocations and complex rearrangements. MinION sequencing resulted in between 14.1-18.3 Gb of data per flow cell, with mean autosomal on-target coverage of 28.4x and off-target read depth coverage of 5.3x.

  Dataset EGAD50000001821

• WGS data of paediatric ETV6::RUNX1 B cell acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM/CRAM files from diagnostic and matched remission (control) samples of five ETV6::RUNX1 ALL patients (ALLT-380, ALLK-114, ALLT-388, ALLT-392, ALLT-394). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using NEBNext® Ultra™ II DNA Library Prep Kit (Cat No. E7645). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002285