1073 results for "2025年12月600642股价走势分析"

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• Array_dataset_ega_box_64

  ATRT expression

  Dataset EGAD00010001546

• DAC Admixture histories of São Tomé e Príncipe

  Contacts: Paul Verdu +33144057317 paul.verdu@mnhn.fr CNRS-MNHN-Université de Paris UMR7206 Eco-anthropology Jorge M. Rocha jrocha@cibio.up.pt CIBIO Short description The Data Access Committee for acess to genotype and sample information used in the article "Nested admixture during and after the Trans-Atlantic Slave Trade in the island of Sao Tome" by Ciccarella M et al.2025 ensures that data-access requests comply with the Informed Consent provided by donors, and with ethical and deontological guidelines with respect to privacy. Research sampling protocols followed the Declaration of Helsinki guidelines and written informed consent was obtained from all volunteer participants involved in the sampling in São Tomé e Príncipe. The study of the São Tomé e Príncipe sample was undertaken with the support and permission of the Provincial Government of the Ministry of Health of the Democratic Republic of São Tomé e Príncipe, and the Provincial Government of Príncipe. Research sampling protocols also followed the French laws of scientific research deontology (Loi n° 2016-483 du 20 avril 2016) and were approved by the French ethics committees and CNIL (Declaration n°1972648).

  Dac EGAC50000000437

• EGAD00010000510

  Matched control samples using HumanOmni1-Quad

  Dataset EGAD00010000510

• EGAD00010000514

  Case samples using SNP 6.0 Array

  Dataset EGAD00010000514

• UK10K_COHORT_TWINS REL-2011-12-01

  UK10K_COHORT_TWINS REL-2011-12-01

  Dataset EGAD00001000194

• WGS of IPMN-PDAC Data

  This study investigates IPMN-PDAC development using whole-genome sequencing (WGS) data from 42 tumours collected from multiple regions and 12 matched normal samples. Sequencing was performed on Illumina platforms with 150 bp paired-end reads.

  Study EGAS50000001182

• INDIA

  We collected PBMCs from 10 Indian and 10 Dutch individuals before BCG vaccination and 10-12 post-vaccination. We assessed the open chromatin profiles under baseline conditions, and the transcriptomic profiles upon stimulation with Influenza and SARS-CoV-2.

  Study EGAS00001006417

• Whole Genome Sequencing of INTERVAL (2019-06-12)

  15x Whole Genome Sequencing of 15,000 individuals from the INTERVAL study cohort, phase III. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-06-12.

  Dataset EGAD00001005086

• RNA sequencing of tumor samples from patients with BPLL

  RNA-Seq was performed on 12 samples of sorted CD19+ tumor cells. RNA-Seq libraries were prepared using the SureSelect Automated Strand Specific RNA Library Preparation Kit as per manufacturer’s instructions (Agilent technologies) and subjected to paired-end (2 x 100 bp) sequencing on HiSeq2000 (Illumina). The files are in FASTQ format.

  Dataset EGAD00001004412

• scRNA-seq raw data

  This dataset contains scRNA-seq fastq files (trimmed for quality and adapters using Trim Galore) for 3739 intestinal plasma cells of known or unknown antigen specificities from in total 12 individuals (4 untreated coeliac disease patients, 3 treated coeliac disease patients, 5 controls). The data was generated using the Smart-seq2 protocol and sequenced on the Illumina NextSeq500 platform with 75 bp paired-end reads.

  Dataset EGAD00001006436

• EGAD00010000160

  Illumina HT 12 IDATS

  Dataset EGAD00010000160

• EGAD00010000508

  Matched control samples using SNP 6.0 Array

  Dataset EGAD00010000508

• EGAD00010000528

  Illumina HumanHT-12 v4 array

  Dataset EGAD00010000528

• Whole-exome sequenicing of Diamond-Blackfan anemia

  Dataset EGAD00001000896

• CNVs analysis

  kidney cancer tissue sample

  Dataset EGAD00010001536

• HipSci HumanHT 12 Expression BeadChip analysis - Usher syndrome and congenital eye defects

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Usher syndrome and congenital eye defects.

  Study EGAS00001002023

• Paired WES and low coverage WGS of osteosarcoma

  Longitudinal genome-sequencing analysis of 12 patients with metastatic or refractory osteosarcoma. The study was approved at the University Hospital Basel, following the approval of the ethical committee for mutational analysis of anonymized samples (“Ethikkommission beider Basel” ref. 274/12). Informed consent was obtained from all 12 patients. All tumor samples were evaluated by an experienced bone pathologist to confirm the diagnosis. WES and low coverage WGS are aligned against the reference genome GRCh37. More details in the associated publication.

  Dataset EGAD00001007509

• HIPO016 - glioblastoma tumour methylation microarray profiling

  Methylation microarray profiling (Illumina Human Methylation 450k and EPIC platforms) of 60 adult glioblastomas. Tumours were subtyped using the approach from Sturm et al. (https://doi.org/10.1016/j.ccr.2012.08.024): 12 IDH, 18 MES, 12 RTK I, 18 RTK II. DNA was prepared, assayed on the microarrays, and raw data computationally processed as described in Capper et al., "DNA methylation-based classification of central nervous system tumours": https://www.nature.com/articles/nature26000

  Dataset EGAD00010001797

• Whole genome sequencing of mature B-cell lymphomas to identify MYC, BCL2, and BCL6 rearrangements

  Whole genome sequencing (WGS) data of 12 tumours was generated on an Illumina NovaSeq or HiSeqX instrument. For frozen samples, libraries were constructed using a PCR-free library construction method. For tumours preserved by formalin fixation and paraffin embedding (FFPE), libraries were constructed with a method that included S1 nuclease treatment. Reads were aligned to the grch37 reference with bwa-mem 0.7.17.

  Dataset EGAD50000000474

• WES of paired gDNAs and PPGL tumor DNA from patients with CCHD-PPGL.

  WES of paired germline DNA (12) and PPGL tumor DNA (14) from peripheral blood/saliva and formalin-fixed paraffin-embedded (FFPE) blocks from surgery, respectively, from patients with congenital heart disease (CCHD) and pheochromocytoma and paraganglioma (PPGL).

  Study EGAS50000000815

• Indonesian Genome Diversity Project 3

  Low coverage whole genome sequences were collected to study the population history in Eastern Indonesia, in particular Wallacea and Papua region. We have sequenced the genomes of 254 individuals from 12 Wallacean and 3 Papuan populations spanning this geographical region.

  Study EGAS50000000447

• Transcriptomic and chromatin accessibility profiling in T cells for the MTOR genetics paper.

  This submission contains raw ATAC and RNA sequencing data from human primary CD4+ and CD8+ T cells, either stimulated or unstimulated with anti-CD3/CD28 Dynabeads, from three healthy donors. It includes 24 paired-end FASTQ files consisting of 12 poly(A)-enriched RNA-seq samples and 12 ATAC-seq samples sequenced on the Illumina NextSeq 500 platform.

  Dataset EGAD50000001307

• DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence CRAM files

  DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence CRAM files

  Dataset EGAD00001004390

• DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence VCF files

  DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence VCF files

  Dataset EGAD00001004389

• Phenotype and Genotype determination of 400 individuals from Northern Germany

  Phenotype determination by SNP-Typing using PCR and snapshotPCR with subsequent fragment analysis. We investigated 400 individuals from Northern Germany and detected up to 12 different SNPs to determine eye, hair and skin colour. More than 1000 different runs on a ABI3130 were performedThis dataset includes:- Phenotype information for 400 samples- Summary and complete genotype calls for 12 SNPs on 400 samples.

  Dataset EGAD00001001315

• DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - phenotypic and family descriptions

  DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - phenotypic and family descriptions

  Dataset EGAD00001004388

• Oxidative phosphorylation is a key ontogenetic feature of monocyte immunometabolism promoting myeloid differentiation after birth

  The dataset consists of 12 samples of monocytes, which were analyzed using RNA-sequencing (RNA-seq). These samples were categorized into four distinct groups, each comprising three samples. The dataset was designed to investigate the transcriptomic and metabolic profiles of monocytes across different age groups and stimulation conditions. 3 neonatal controls, 3 neonatal LPS stimulated, 3 adult controls and 3 adult LPS stimulated samples.

  Dataset EGAD00001011340

• Multi-Region WES of Metastatic Colorectal Cancer

  In order to reconstruct the evolutionary history of metastatic colorectal cancer, we performed whole-exome sequencing of 12 metastatic colorectal cancer patients for whom the primary tumor and matched distant metastases to the brain (n=10) and liver (n=2). For 8 of the 12 patients, multiple regions (n=3-7) of the primary tumor and distant metastases were sequenced.

  Dataset EGAD00001004896

• Whole exome sequencing of peripheral T-cell lymphoma (PTCL)

  Dataset EGAD00001000659

• AML scRNA-seq

  Dataset EGAD00001006537

• Revision Experiments UMI

  Revision Experiments UMI

  Dataset EGAD00001010310

• Frequent post-treatment monitoring of colorectal cancer using individualized ctDNA validated by multi-regional molecular profiling

  Purpose: Circulating tumor DNA (ctDNA) analysis has been proposed as an approach for prediction of post-treatment patient outcomes. However, whether a single platform will provide optimal information in all patients or alternatively a patient-specific monitoring approach based on assessment of mutations in the primary tumor from that patient remains an urgent question. Experimental Design: We conducted multiregional sequencing of 42 specimens of 14 colorectal tumors (Stage III and more) from 12 patients, including two double cancer cases, to identify the full spectrum of mutational heterogeneity and identify aberrations that could be used to develop personalized ctDNA assays. Results: ?Founder? mutations that occur in all regions of the sample were identified in 12/14 (85.7%) tumors. Subsequent phylogenetic analysis of each tumor showed that 12/14 tumors (85.7%) carried at least one ?truncal? mutation. Most founder and truncal mutations exhibited higher variant allele frequency (VAF) than ?non-founder? and ?branch? mutations. In addition, both founder and truncal mutations were more likely to be detected as ctDNA than non-founder and branch mutations. Synchronized ctDNA dynamics of multiple mutations suggested those mutations from the same clonal origin. For 10/12 patients (83.3%) with nearly 1,000 days of post-operative observation, the validity of frequent personalized ctDNA monitoring was confirmed in terms of early relapse prediction, treatment efficacy, and non-relapse corroboration. Conclusions: Personalized ctDNA monitoring based on aberrations with a high VAF in the primary tumor site should be explored in larger prospective clinical trials to determine the full clinical validity.

  Study JGAS000243

• transcriptomics

  Transcriptomics analysis results

  Dataset EGAD00010001659

• ProteomicAnalysis(DIA)ofmuscleinvasivebladdercancerpatient-derivedxenografts

  Accesstoproteomicfiles(DIA)ofMIBCpatient-derivedxenografts(N=8)

  Dataset EGAD00010002512

• Methylation_gDNA_wbc

  Genome-wide CpG methylation information of genomic DNA samples from white blood cells

  Dataset EGAD00010002586

• HumanCytoSNP12-2-1

  HumanCytoSNP-12 v2.1 on tissue DNA

  Dataset EGAD00010002091

• WGS of 14 paired hepatocellular carcinomas

  Dataset EGAD00001000749

• RNA-seq

  RNA-seq of PDXs

  Dataset EGAD00001001862

• Pharmacogenomics of HIV Therapy - Atazanavir Bilirubin-related Side Effects

  This is an evaluation of genetic associations with atazanavir (ATV) discontinuation for bilirubin-related causes within 12 months of treatment. Patients were treated at an HIV primary care clinic in Nashville TN from 1998 to 2012. A previously known SNP in UGT1A1 (rs887829) was used to define metabolizer genotypes (extensive, intermediate, slow metabolizer). Over 500,000 SNPs from genome-wide genotyping were used to define MDS (Multidimensional Scaling) coordinates to account for population stratification. Patients were defined as cases if they discontinued ATV for bilirubin-related causes within 12 months of treatment, otherwise they were defined as controls if they did not stop treatment. Among 321 evaluable patients, 15 (4.6%) had bilirubin-related atazanavir discontinuation within 12 months. Homozygosity for rs887829 T/T was present in 28.1% of black, 21.4% of Hispanic, and 8.6% of white patients. Among all patients the hazard ratio (HR) for bilirubin-related discontinuation with T/T versus C/C genotype was 7.3 (95% C.I.: 1.7 to 31.5; p = 0.007). Among 152 white patients the HR was 14.4 (95% CI: 2.6 to 78.7; p = 0.002), but among 153 black patients the HR was 0.8 (95% C.I. 0.05 to 12.7; p = 0.87).

  Study phs001484

• A Therapeutic Vaccine for Fibrolamellar Hepatocellular Carcinoma

  Fibrolamellar hepatocellular carcinoma (FLC) is a rare form of liver cancer affecting 33 children and young adults that is driven by a chimeric protein, DNAJ-PKAc. We conducted a phase 1 clinical trial of a therapeutic vaccine targeting DNAJ-PKAc 38 (FLC-Vac), in combination with nivolumab and ipilimumab, in children and adults with advanced FLC. Among 16 patients enrolled, 12 completed the vaccine priming phase and were evaluable for both immunological and clinical endpoints. Grade 3 treatment-related adverse events were reported by six patients (37.5%). DNAJ43 PKAc-specific T cell responses were detected in 9/12 patients after treatment. In the subset of patients who completed the initial priming phase the disease control rate (DCR) was 75% (9/12), with three partial responses (25%). All patients with clinical responses also had DNAJ-PKAc specific T cell responses, from which we identified multiple class II-restricted T cell receptors (TCRs) with specificity for DNAJ-PKAc. Correlates of response included both functional neoantigen reactivity and changes in TCR repertoire features over time. Immune escape in two patients corresponded with immune exhaustion rather than neoantigen escape or HLA loss.

  Study phs003970

• native_american_pops_Axiom_Human_Origins

  Sample genotyped with Axiom Human Origins (Affymetrix)

  Dataset EGAD00010001803

• DATA FILES FOR SJMEL-WGS

  DATA FILES FOR SJMEL-WGS

  Dataset EGAD00001001032

• Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Atherosclerosis Risk in Communities Study (ARIC)

  Cohort Description The Atherosclerosis Risk in Communities (ARIC) study began in the mid-1980s with the initial aims being to describe the presence of subclinical atherosclerosis, the progression of atherosclerosis to clinical cardiovascular disease (CVD), and the association of novel risk factors with CVD. ARIC recruited its cohort of men and women aged 45-64 in 1987-89 from four communities (Forsyth County, NC; Jackson, MS; suburban Minneapolis, MN; and Washington County, MD). As of 2025, ARIC counts over 4,000 participants.Data Submitted Wave 1 questionnaire data includes 356 variables for up to 5763 ARIC participants in C4R. Wave 2 questionnaire data includes 367 variables for up to 5000 ARIC participants in C4R. Wave 3 questionnaire data includes 81 variables for up to 3450 participants in C4R.Dried Blood Spot/Serosurvey data includes 8 variables for up to 2437 ARIC participants in C4R. Derived data includes 62 variables for up to 18765 observations. Phenotype data includes 163 variables for up to 5937 ARIC participants in C4R. Brain MRI data includes 13 variables for up to 2550 participants in C4R.HCU data includes 21 variable for up to 631 ARIC participants in C4R.Lung CT data includes 15 variables for 1329 ARIC participants in C4R.Neurocognitive data includes 16 variables and 49826 observations.Serosurvey data includes 20 variables for 1707 ARIC participants in C4R.

  Study phs002988

• Trans-ethnic genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation

  We carried out a trans-ethnic genome-wide association and replication study of blood pressure phenotypes amongst up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 novel loci to be associated with blood pressure (P=3.9x10-11 to P=5.0x10-21). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that at some of the loci identified DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 novel loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7, TBX2) function. The novel and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, cardiovascular and all-cause mortality (P=0.04 to 8.6x10-6). Our results provide new evidence for the role of DNA methylation in blood pressure regulation.

  Study EGAS00001001427

• Expression array

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed.
This dataset contains expression array data for 32 patients of the screening cohort with 8 of them having paired normal tissue plus an additional relapse tumor/normal pair of one of those 8 patients and a patient only with normal tissue. Data was generated on a HumanHT-12 v4 Bead Array (Illumina) and is stored in IDAT file format.

  Dataset EGAD00010002596

• RNA-Seq data from tumor samples collected from 12 UTSW translocation renal cell carcinoma (tRCC) patients.

  This study investigates differentially expressed genes associated with the progression of translocation renal cell carcinoma (tRCC) by analyzing RNA-Seq data from 23 tumor samples obtained from 12 patients. The samples were collected from affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital and Children’s Medical Center. RNA isolated from tumor samples was sequenced using the Illumina platform.

  Dataset EGAD50000000172

• Single Cell, Whole Genome Analysis of the Aging Human Cardiomyocytes

  In this study we have sequenced single cardiomyocytes from 12 individuals (ages from 0.4 to 82 yrs.). We have identified and characterized the somatic single-nucleotide variants (sSNVs). Our study indicates that cardiomyocyte sSNVs increased with age with distinctive mutational signatures.

  Study phs002284

• WES analysis of DMD-ASD, DMD-ID and DMD-Control individuals for de novo and rare risk variants analysis

  This project generated a whole-exome sequencing (WES) dataset of 83 boys with a pathogenic variant in the DMD gene, along with WES data from the parents of 38 of them, totaling 159 samples. In addition to DMD, 12 boys also had ID (12 DMD-ID samples), 36 boys had ASD (DMD-ASD samples) and 35 did not present ID or ASD diagnosis (DMD-Control samples).

  Dataset EGAD50000001113

• CRISPRi/a of GATA2/NR4A2/SOX17 upon spontaneous iPSC differentiation

  Arrayed CRISPR screens, modulating the expression of key lineage TFs GATA2 (mesoderm), SOX17 (endoderm), and NR4A2 (neuroectoderm) in hiPSCs via CRISPR interference or activation over a time-course of spontaneous differentiation (days cultured in vitro: 0, 4, 12, and 18).

  Study EGAS50000000819

• WGS Data from 42 Multi-Region Sampled IPMN-PDACs and 12 Matched Normal Samples

  This dataset contains whole genome sequencing (WGS) data from 42 IPMN-PDAC and 12 normal samples, with tumours collected from multiple regions within each tumour to capture intra-tumour heterogeneity. Tumour and matched normal samples were sequenced to study somatic mutations, structural variants, copy number alterations, mutational signatures and clonal evolution during IPMN-PDAC progression. The sequencing was performed using Illumina NovaSeq instrument with 150 bp paired-end reads.

  Dataset EGAD50000001687

• cryopreserved PBMC

  This dataset consists of 12 RNA samples derived from peripheral blood mononuclear cells (PBMCs) collected from three healthy donors. The samples cover four experimental conditions: fresh PBMCs (ID: 517210–517212), PBMCs subjected to a single freeze–thaw cycle (ID: 517213–517215), PBMCs refrozen in freezing mix (ID: 517216–517218), and PBMCs refrozen in TRIzol (ID: 517219–517221). Each sample is provided as a FASTQ file, and RNA sequencing was performed using the Illumina platform. This dataset enables the assessment of cryopreservation effects on PBMC transcriptomic profiles.

  Dataset EGAD50000001703

• Screening of 2.5 million SNPs in 142 samples from the western Mediterranean area

  The analysis of 2.5 million SNPs in 142 samples from the western Mediterranean area, including southern Spain, Andalusia (Huelva: 35 samples, Granada: 35), southern Portugal (36 samples) and Moroccan Berbers (Asni: 15, Bouhria: 12 and Figuig: 9).

  Study EGAS00001003901

• WTCCC2 Reading and Mathematics (RM) samples

  A WTCCC2 project genome-wide association study for reading and mathematics ability in 3665 12-year-old individuals from the UK, genotyped on the Affymetrix 6.0 array. Details of the WTCCC2 analysis can be found in Davis et al. [Nat. Commun. 2014 July;5:4204]

  Study EGAS00001000886

• Placental multi-omics data-mining in Intra-Uterine Growth Restriction

  Methylomics and transcriptomics array-based analysis of 36 placentas: 28 with IUGR (Intra-Uterine Growth Restriction) vs. 8 control pregnancies. Methylomics data were obtained using Illumina HumanMethylation-450k microarrays. Transcriptomics data were obtained using Illumina HumanHT-12 v4 Expression BeadChips.

  Study EGAS00001003467

• Somatic mutation and clonal evolution in the human pancreas - WGS (2019-12-17)

  In this study we aim to characterise the landscape of mutation and clonal selection in the human pancreas. The study combines targeted sequencing and whole-genome sequencing of microbiopsies from the pancreas. The range of patients studied will include healthy individuals, both smokers and non-smokers, and patients with pancreatic ductal adenocarcinoma. This dataset contains all the data available for this study on 2019-12-17.

  Dataset EGAD00001005751

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MC2392, on genome GRCh38

  ChIP-Seq data for 2 Acute Promyelocytic Leukemia - MC2392 sample(s). 14 run(s), 12 experiment(s), 12 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002406

• BLUEPRINT release August 2015, ChIP-Seq for plasma cell, on genome GRCh38

  ChIP-Seq data for 2 plasma cell sample(s). 13 run(s), 12 experiment(s), 12 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001470

• BLUEPRINT release August 2015, ChIP-Seq for neutrophilic metamyelocyte, on genome GRCh38

  ChIP-Seq data for 4 neutrophilic metamyelocyte sample(s). 18 run(s), 12 experiment(s), 12 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001495

• omnix_himalaya

  Himalayan population genetic study raw data (Himalaya)

  Dataset EGAD00010001470

• Weige_450k_Control

  Control human dermal fibroblasts from patient forearm

  Dataset EGAD00010001879

• Weige_450k_Case

  Case human dermal fibroblasts from patient forearm

  Dataset EGAD00010001880

• A Phase I/II Trial of T Cell Receptor Gene Therapy Targeting HPV-16 E7 for HPV-Associated Cancers

  This is a phase I clinical trial testing the safety and efficacy of gene-engineered T cells expressing a T-cell receptor targeting an HLA-A*02:01-restricted epitope of HPV-16 E7 (E7 TCR T cells) in patients with metastatic HPV-16+ epithelial cancers. A total of 12 patients were treated. The maximum tested dose was tolerated. Side effects were most consistent with the expected toxicities of the lymphocyte-depleting conditioning regimen and high-dose aldesleukin. Six of the 12 patients demonstrated objective clinical responses. Translational studies of the infused T cell characteristics did not correlate strongly with clinical response. Genomic defects in the targeted peptide-HLA complex did demonstrate definitive mechanisms of resistance in some patients.

  Study phs002286

• Pilot_experiment_on_functional_genomics_in_osteoarthritis_RNA

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). In this pilot we will assess the feasibility of the approach in the relevant tissue. We will obtain diseased and non-diseased tissue (cartilage and endochondral bone) following TJR, coupled with a blood sample, from 12 patients. We will characterise the 12 pairs of diseased and non-diseased tissue samples in terms of transcription (RNASeq) The pilot will help assess the feasibility of isolating sufficient levels of starting material for the different approaches, and will instigate the development of analytical approaches to synthesising the resulting data.

  Study EGAS00001001203

• RNAseq of PC-9 and KHM-3S with and without tarceva

  Dataset EGAD00001000843

• PDAC CT WEX PDX1

  Whole Exome Sequencing on PDAC PDX1 parental sample and 12 clones.

  Dataset EGAD00001004580

• EGAD00010000560

  SNP array of 7 HCCs and matched background liver in children with bile salt export pump deficiency

  Dataset EGAD00010000560

• Array_data

  Array data from a family with high prevalence of psychosis

  Dataset EGAD00010002030

• RNA-seq from Glioblastoma treated with Indisulam

  The dataset includes RNA-sequencing results from four patient-derived glioblastoma cell lines treated with DMSO (vehicle control) or the splicing modulating-drug indisulam (at 6 and 16 hours), resulting in 12 RNA-seq samples. Paired-end sequencing produced 24 FASTQ.gz files. The RNA libraries were prepared using PolyA selection and ERCC spike-ins and sequenced on a NovaSeq platform. This dataset supports the analysis of drug-induced transcriptomic changes and the prediction of subsequent non-canonical tumor-specific antigens (ncTSAs) using the NovumRNA pipeline.

  Dataset EGAD50000000957

• Transcriptional data of human isogenic iPSCs

  This dataset contains bulk RNA-seq data from 12 autosomally isogenic human iPSCs. Three biological replicas from XXY (sample ID 419295-7), XX (sample ID 419298-419300), XY (sample ID 419302, 419305-6), and XO (sample ID 419308, 419310, 419312) hiPSC. RNA for this dataset was collected using Trizol method, and polyA library type was implemented. The libraries were sequenced using Illumina device. The sample reads are deposited as fastq files. Analysis have been done using reference alignment to GRCh38 reference genome.

  Dataset EGAD50000001361

• Targeted gene expression analysis on FFPE specimen from NSCLC patients

  This study measured the expression of a panel of over 300 cancer immunotherapy-relavant genes in tumors after neoadjuvant chemoimmunotherapy. It was performed on RNA from FFPE tumor tissue. Differential gene expression analysis was performed between patients achieving or not achieving an event-free survival of 12 months.

  Study EGAS50000001140

• RNA-Seq on OCIAML-22 Fractions

  The donor AML patient (unsorted) that was used to generate OCI-AML22 was expanded for the indicated number of days (Donor: 0 day, 12d: 12 days, 2m: 2 months, 3m: 3 months), then sorted for the indicated fraction (CD34p: CD34+; CD34m: CD34-, CD38m: CD38-, CD38m: CD38-).

  Study EGAS00001006512

• Mapping genetic variants underlying gene regulation in healthy intestinal cell types to identify novel IBD drug targets (2020-05-12)

  Biopsies from the terminal ileum and rectum of healthy individuals are digested on ice to single cells and processed for single-cell RNA-sequencing (10X Genomics and Illumina) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2020-05-12.

  Dataset EGAD00001006139

• Single-cell bam files and RNA sequencing of viral RNA stocks

  244 infected single-cell alveolar bam files, 48 empty well bam files, and 52 RNA sequencing of amplicons (4 SARS-CoV-2 variants with 12 batches and 4 viral variants pool samples). 244 alveolar single cells were captured over 12 experimental batches and experimental condition is written in metadata uploaded as "infected_cells_final_revision.csv". on github (https://github.com/twkim-0510/SARS-CoV-2_viral_competition). Each bam file name corresponds to the sample_name column of the metadata.

  Dataset EGAD00001009711

• BLUEPRINT release August 2015, ChIP-Seq for macrophage, on genome GRCh38

  ChIP-Seq data for 12 macrophage sample(s). 49 run(s), 49 experiment(s), 49 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001576

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (bulk RNA)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. RNAseq (BAM files) 12 Barrett's samples 12 normal oesophageal samples 11 normal gastric cardia samples

  Dataset EGAD00001006882

• Primary angiosarcoma Whole Genome Sequencing

  Whole genome sequencing of primary angiosarcoma

  Dataset EGAD00001001266

• MSI-Exome-DAC Team Microsatellites Instability and Cancer, INSERM Hospital Saint-Antoine, Paris 12, France Carte d'identité des tumeurs, French league against cancer, Paris France

  Dac EGAC00001000665

• chr12_allsamples_imputated

  Chromosome 12 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002517

• Colorectal cancer cells possess an equipotent capacity to enter a developmental pausing-like state to survive chemotherapy

  Dataset EGAD00001006847

• Exome sequencing of patients with structural brain malformations

  Exome sequencing of 12 DNA samples obtained from patients with structural brain malformations.

  Dataset EGAD00001000345

• ICGC prostate cancer RNA sequencing

  ICGC prostate cancer RNA sequencing

  Dataset EGAD00001000305

• ICGC prostate cancer MBD sequencing (DNA methylation)

  Dataset EGAD00001000632

• Sample metadata

  Sample metadata for this experiment. Includes treatment and donor derivation information.

  Dataset EGAD50000000827

• TCR β-chain repertoire characterization of regulatory and conventional T cells in breast tumors from breast cancer patients.

  Dataset EGAD00001006428

• BRCA Mutation Status Shapes the Microenvironment of Pancreatic Adenocarcinoma

  This study was established in order to address how the stromal landscape is influenced by BRCA-mutated and BRCA Wild-type (WT) pancreatic ductal adenocarcinoma (PDAC). A primary cohort of 12 PDAC patients (7 BRCA-WT and 5 germline BRCA-mut) was analyzed by laser-capture microdissection, RNA-sequencing and multiplexed immunofluorescence.

  Study phs002994

• Methylome of memory B cells with autoproliferation in MS

  Methylome of resting/hi and autoproliferating/Dim memory B cells in Multiple sclerosis patients. In brief, non-proliferating (CFSEhi) and AP+ (CFSEdim) CD19+ CD27+ B cells from PBMCs of 6 natalizumab-treated female RRMS (NAT) patients were sorted following 7 days of autoproliferation. Methylome libraries for 12 samples were constructed by applying the post-bisulfite adaptor tagging (PBAT) method on lysed cells and sequencing was conducted on Illumina NovaSeq 6000. CpGs with minimum 10X coverage were used for differential methylation position (DMP) analysis.

  Dataset EGAD50000001269

• Whole-genome sequencing data of poorly differentiated thyroid carcinomas and matched blood from six patients

  This dataset contains raw sequencing reads in FASTQ format from 12 samples, comprising paired tumour and matched blood DNA from six patients diagnosed with poorly differentiated thyroid carcinoma (PDTC). Genomic DNA was extracted from fresh-frozen tumour tissue and peripheral blood using standard protocols. Whole-genome sequencing was performed on the Illumina HiSeq X Ten platform, generating paired-end reads at an average depth of approximately 20X. These data support investigations into the somatic mutational landscape and genomic alterations associated with PDTC.

  Dataset EGAD50000001628

• Oxford Nanopore long-read sequencing data of high-grade serous ovarian cancer

  This dataset comprises whole-genome Oxford Nanopore long-read sequencing data from six high-grade serous ovarian cancer (HGSOC) patients, including cryopreserved, pre-treatment tumor tissues and matched peripheral blood samples (12 samples in total). High-molecular-weight DNA was prepared using the SQK-LSK114 Ligation Sequencing Kit and sequenced on FLO-PRO114M flow cells (R10.4.1). Basecalling was conducted using the super-accurate (SUP) model, enabling simultaneous detection of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). The dataset includes BAM files containing base modification information for downstream genomic and epigenomic analyses.

  Dataset EGAD50000001509

• Oxford Nanopore RNA sequencing for HLA typing

  A targeted RNA-based method for typing of 12 classical HLA genes using Oxford Nanopore sequencing. In the method, were enriched HLA genes from cDNA of 50 individuals using gene-specific reverse primers. The library molecules were then barcoded, pooled into 2 separate gene pools, and sequenced on MinION R9.4 SpotON flow cells.

  Study EGAS00001004918

• Targeted sequencing data and shallow whole genome sequencing data of Follicular lymphoma.

  Contain data of 2 studies 1: 82 nodal stage 1 FL cases and 139 stage III/IV cases 2: 44 watch and wait stage III/IV and 46 Immediate treatment stage III/IV targeted sequencing data of 369 genes and 12 translocation regions whole genome shallow sequencing data

  Study EGAS00001005755

• Pediatric B-cell precursor acute lymphoblastic leukemia samples with very early relapse

  In this study we performed a genomic analysis of diagnosis-relapse pairs of 12 children who relapsed very early, followed by a deep-sequencing validation of all identified mutations. In addition, we included one case with a good initial treatment response and on-treatment relapse at the end of upfront therapy.

  Study EGAS00001005615

• Personalised Mapping of Tumour Development in Synchronous Colorectal Cancer Patients

  We performed an in-depth characterisation of 12 tumours from 3 syCRC patients by analysing histopathological, whole genome sequencing and RNA-sequencing data. We assessed the extent of genetic overlap between synchronous tumours and examined associations between clinicopathological information and the molecular, microbial and immune features of each tumour genome.

  Study EGAS00001004413

• Facioscapulohumeral dystrophy transcriptome signatures correlate with different stages of disease and are marked by different MRI biomarkers

  This project includes RNA-sequencing data from human FSHD and control skeletal muscle biopsies. This project includes data from 28 FSHD patients (total 37 samples, including vastus lateralis and tibialis anterior muscles) and 12 control individuals (total 24 samples, including vastus lateralis and tibialis anterior muscles).

  Study EGAS00001005782

• PhIP-seq of Japanese patients with SLE

  Bacteriophage Immunoprecipitation Sequencing (PhIP-Seq) datasets of three eHHV-6B-positive SLE patients (three technical replicates), six eHHV-6B-negative SLE patients (three technical replicates), and a negative control lacking sera or plasma (12 technical replicates; Illumina NextSeq) and sequencing data of HHV-6 peptide phage library (two technical replicates; Illumina NextSeq).

  Study EGAS00001007955

• 12 Pediatric B-cell precursor acute lymphoblastic leukemia samples with very early relapse

  Sequencing data (BAM/CRAM) of diagnosis-relapse pairs of 12 children who relapsed very early, followed by a deep-sequencing validation of all identified mutations.

  Dataset EGAD00001008309

• DIPG_ICR_WES

  Whole exome sequencing of 6 tumour and normal pairs of diffuse intrinsic pontine glioma (DIPG)

  Dataset EGAD00001000706

• SNParray_Human_blastocyst_samples

  Single blastomeres from blastocyst and familial samples for haplotyping and copy-number profiling via SNP array

  Dataset EGAD00010002220

• Linked-reads for Juvenile Pilocytic Astrocytomas

  Matched tumor-normal data for 6 JPAs. Generated using 10X Genomics Linked-reads

  Dataset EGAD00001011114

• GEP_DKFZ_JMML_DBL

  Gene expression analysis from primary human JMML samples using Illumina Human HT-12 v4

  Dataset EGAD00010001430

• SNParray_PGT_samples_scGBS

  PGT samples for haplotyping and copy-number profiling via SNP array

  Dataset EGAD00010002169