2200 results for "盛和资源+机构评级+2026年3月最新"

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• PCCRC versus prevalent CRC

  To analyse genome wide DNA copy number changes in combination with mutation status of CRC-related genes, CIMP and MSI, in order to explore the biology of PCCRCs. Formalin-fixed, paraffin-embedded samples from 122 PCCRCs and 98 prevalent CRCs collected in 3 different hospitals in the region of South Limburg, the Netherlands, were used in this study. DNA was extracted for molecular analysis. Labels have been updated.

  Dataset EGAD00001006987

• Chromatin accessibility (ATAC-seq) of human acute leukemias and healthy donors

  ATAC-seq of 79 primary samples obtained from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). ATAC-seq of CD34+ HSPCs from 3 healthy donors is also included.

  Dataset EGAD00001011050

• WXS Normal Samples Javelin head and neck 100

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

  Dataset EGAD00001011321

• Gene Expression Study of Individuals with Sex Chromosome Aneuploidies

  Males and females show dramatic differences in their vulnerability to the same diseases. For example, compared to men, lupus is six times more prevalent, thyroid cancer is three times more prevalent, and unipolar depression is twice as prevalent in women. Diseases with a strong male bias include autism (5:1), dilated cardiomyopathy (3:1), and ankylosing spondylitis (5:1). Historically, such differences have been attributed solely to extrinsic factors such as circulating sex hormones or environmental influences. We hypothesized that intrinsic factors - genetic differences between XX and XY cells - have unappreciated biological consequences throughout the body and contribute to sex differences in disease incidence and severity. This hypothesis stems from our long-term effort to sequence the sex chromosomes of diverse mammalian species, which has identified a set of homologous genes on the X and Y chromosomes that are dosage-sensitive, expressed throughout the body, and encode regulators of chromatin modification, transcription, translation, and protein stability. These X- and Y-encoded genes differ in sequence and expression pattern, which likely manifests in genome-wide differences in gene regulation between XX and XY cells and influences all aspects of human biology, including sex differences in disease susceptibility. These hard-wired molecular sex differences have been largely overlooked and understudied, representing a significant gap in our knowledge of human biology.The gene expression study of individuals with sex chromosome aneuploidies takes advantage of natural human variation in sex chromosome number, i.e. sex chromosome aneuploidy, to investigate alterations in genome-wide gene expression that correlate with changes in X- and Y-chromosome dosage. We analyzed samples from 114 individuals with a variety of sex chromosome aneuploidies, including 45,X; 47,XXY; 47,XYY; 47,XXX; 48,XXYY; and 49,XXXXY. We generated lymphoblastoid cell lines (LCLs) from blood samples and, in some cases, fibroblast cultures from skin biopsies. We supplemented our collection with previously-derived cell lines. To evaluate gene expression, we performed deep profiling of the transcriptome (RNA-seq) from these LCLs and fibroblasts. We performed parallel analyses on samples collected from 62 control 46,XX and 46,XY individuals, 6 individuals with trisomy 21, and 14 individuals with structural variations of the X and Y chromosomes. In addition, we performed CRISPRi knockdowns on 3 of the 46,XX and 3 of the 46,XY fibroblast samples for the homologous transcription factors ZFX and ZFY, encoded on the X and Y chromosomes, respectively.In the April 2024 update, we added RNA-seq datasets derived from isolated CD4+ T cells and monocytes from 76 and 72 adults, respectively, with the following sex chromosome constitutions: 45,X; 46,XX; 46,XY; 47,XXX; 47,XXY; 47,XYY. These individuals are largely a subset of the same cohort described above. In addition, we performed RNA-seq on in-vitro stimulated CD4+ T cells with the following sex chromosome constitutions: 45,X; 46,XX; 46,XY; 47,XXY.In the August 2024 update, we added RNA-seq datasets generated from the following: 1) LCLs derived from individuals with AZFa deletions of the Y chromosome, 2) DDX3X and DDX3Y knockdown (via CRISPRi) in XY fibroblasts, and 3) 5-ethyl uridine (5-EU) treatment in XY and XYYYY LCLs.

  Study phs002481

• SC_DDD-G-3

  Unfiltered genotype data for DDD Study trios (patient and parents) (N=2,166 samples), some of which were used for replication of neurodevelopmental disorder polygenic risk (Niemi et al., Nature 2018). Samples were genotyped on the Illumina HumanOmniExpress BeadChip

  Dataset EGAD00010001602

• iPSC and iPSC derived pericytes

  Bulk RNA sequencing of iPSCs and iPSC derived pericytes from three cell lines MNZTASi019-A, MNZTASi021-A and MNZTASi022-A. Data includes one iPSC data set per cell line and iPSC derived pericyte differentiations per cell line (3 differentiations from MNZTASi019-A and MNZTASi021-A, 2 from MNZTASi022-A). RNA-seq data was generated using an Illumina Stranded mRNA 150bp paired-end library preparation.

  Dataset EGAD50000000255

• CITE-seq AdaptNK

  CITEseq was performed as outlined in Biolegend ‘TotalSeqTM-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol’ with minor modifications, using Biolegend oligo-conjugated antibodies and streptavidin TotalSeq reagents. Briefly, ADAPT-NK cells were stained with CD56-biotin mAb (Miltenyi, clone REA196), followed by TotalSeq antibodies and streptavidin-PE and Live/Dead Aqua (Invitrogen). Cells were subsequently sorted for viable CD56+ cells by flow cytometry.

  Dataset EGAD50000000329

• PBMC scRNA-seq data using 10X Genomics platform

  Matrices of counts from single-cell RNA-seq data and single-cell CITE-seq data collected from 16 patients enrolled in GO30103 trial, and the cell level annotation. Specifically, PBMCs at C1D1, C1D15 (2 weeks after treatment), C2D1 (3 weeks after treatment) and C4D1 (9 weeks after treatment) were collected and subject to 10x Genomics protocol. Associated metadata also included.

  Dataset EGAD50000000370

• paired-end FASTQ files from the study: Identification of the cause of juvenile parkinsonism in a case_SYNJ1

  The dataset consists of three samples: two controls and one case of juvenile Parkinsonism. Whole Exome Sequencing (WXS) was performed on these samples using hybrid selection for library preparation. Sequencing was carried out on the Illumina NextSeq 500 platform. For each sample, two FASTQ files containing paired-end reads (R1 and R2) were generated. The data deposited consists of the corresponding FASTQ files.

  Dataset EGAD50000000413

• Dataset for the manuscript of Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing

  Dataset for the manuscript Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing. Contains fastq files for 4 brain samples obtained from short-read NovaSeq 6000 v1.5 Illumina and long-read Oxford Nanopore PromethION sequencing. Single-cell suspensions were generated using 10x Genomics Chromium Next GEM Single Cell 3'Kit v3.1

  Dataset EGAD50000000768

• DNA methylation changes associated with hyperglycemia in type 1 diabetes

  This dataset includes DNA methylation profiles from 112 young with Type 1 Diabetes (T1D) at T1D diagnosis, who were longitudinally monitored for hyperglycemia over an average duration of 3 years. These datasets were generated using whole-genome bisulfite sequencing. It includes 1872 fastq files (i.e. 936 paired-end fastq files) generated through 150 bp paired-end sequencing on Illumina HiSeqX.

  Dataset EGAD50000000545

• Whole Genome DNA Methylation MPI

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Catalog No. 30024), the EZ DNA Methylation-Gold Kit (Zymo, D5005) and DNA Clean & Concentrator-5 (Zymo, D4013), following the instruction manual Accel-NGS® Methyl-Seq DNA Library (Revision 160510). Paired-end libraries (2 × 150 bp) were sequenced on a NovaSeq 6000 instrument.

  Dataset EGAD50000001139

• Single-cell Transcriptome Analysis of Plasma Cells Across the Disease Spectrum of Multiple Myeloma

  This dataset includes FastQ files of single-cell RNA sequencing data of 5' GEX and VDJ libraries from CD138+ plasma cells enriched from 72 bone marrow aspirates from patients diagnosed with a monoclonal gammopathy from the multiple myeloma spectrum, including MGUS (n=13), SMM (n = 22), NDMM (n = 17), RRMM (n = 15) and PCL (n = 2); and 3 controls.

  Dataset EGAD50000001179

• Single cell RNA sequencing of co-culture of human organoids with polarized pro-inflammatory (M1) or anti-inflammatory (M2) macrophages

  In order to know if the mechanisms we identified in mice – demonstrating that macrophages are able to orchestrate the intestinal regenerative process – are conserved in humans we develop a co-culture system with human intestinal organoids and human polarized macrophages. We co-culture human organoids with pro-inflammatory or anti-inflammatory macrophages for 48h. On day 3 cells were collected to perform single cell RNA sequencing.

  Dac EGAC50000000270

• Targeted DNA sequencing of 44 urothelial cancer samples from 34 Lynch syndrome patients

  Targeted Illumina sequencing of 41 tumor tissue samples and 3 urine tumor DNA samples from 34 patients with Lynch syndrome associated urothelial cancer. Target capture was performed using the UroScout hybridization capture panel targeting the coding regions of 25 urothelial cancer genes. Sequencing libraries were constructed using the Twist Biosciences Enzymatic Fragmentation DNA Library Prep kit. Sequencing was performed using an Illumina NovaSeq 6000 instrument with 2x150 bp paired sequencing.

  Dataset EGAD50000001220

• Whole genome sequencing data of paediatric KMT2A-rearranged acute lymphoblastic leukemia

  Whole genome sequencing data from infant (<1 y) paediatric (< 18 y) KMT2A-rearranged acute lymphoblastic leukemias. Dataset includes fastq and BAM files from diagnostic and remission (control) samples of 3 patients. Dataset consists of two experiments depending on library preparation method; "Experiment 1" is made using normal WGS library preparation (pcr+), and "Experiment 2" is made using pcr-free library preparation method.

  Dataset EGAD50000001568

• This dataset includes FASTQ for single-nucleus RNA-seq of normal controls, and multiple system atrophy (MSA) or Parkinson's disease (PD) patients.

  The dataset includes more than 130k nuclei isolated using 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1. In total, 30 samples are included from 10 controls, 8 MSA (including one sample that was omitted during QC), or 12 PD patients. Samples were sequenced on Illumina Novaseq 6000 or NextSeq 550 instruments.

  Dataset EGAD50000002041

• Transcriptional profiles of Kleefstra syndrome (EHMT1 and EHMT2) and healthy fibroblasts

  This dataset contains FASTQ files from RNA sequencing (RNA-seq) of fibroblasts derived from a healthy donor (control), a patient with Kleefstra syndrome (KSP), and a patient carrying a pathogenic variant in EHMT2 (P2). Ribosomal RNA was removed using an RNase H–based depletion method, and strand-specific libraries were prepared for paired-end sequencing on the MGI DNBSEQ PE100 platform.

  Dataset EGAD50000002343

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX006_PBC04106_001

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq

  Dataset EGAD00001005163

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX021_SA854_002

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq

  Dataset EGAD00001005142

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX038_VOA11267_002

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 3 samples; filetype=fastq

  Dataset EGAD00001005165

• Longitudinal ctDNA in Uveal Melanoma

  This dataset contains data from 11 uveal melanoma patients. Plasma samples were collected at baseline, 2-weeks, 3-, 6-, and 12-months post treatment (surgery/radiation). Samples underwent targeted panel, shallow whole genome, and cfMeDIP sequencing. A total of 46 plasma samples, 7 tumours, 11 buffy coats, and 10 healthy controls are included.

  Dataset EGAD00001008998

• RNA-Seq of response to Tozinameran vaccination in individuals with KTx/dialysis or healthy controls.

  Low-input RNA-Seq (~200 cells per sample) of CD4+ T cells in patients with kidney transplants, dialysis, or healthy controls after the second dose of Tozinameran COVID-19 vaccine. RNA-Seq was performed using the Smart-Seq v4 ultra-low input protocol. The dataset includes 4 healthy control samples, 3 kidney transplant recipients, and 4 patients undergoing dialysis.

  Dataset EGAD00001007689

• RNA-seq from time-course experiment treating cells for 72h

  RNA sequencing from MSTO-211H cell line cultures treated for 72h with vehicle solution, palbociclib 250nM, or abemaciclib 250nM (N = 3, each). RNA-seq prepared using TruSeq Stranded mRNA libraries and sequenced with Illumina HiSeq 4000. Data is in raw fastq format, paired end. Some samples have been split in two lanes, with a final count of 24 fastq files.

  Dataset EGAD00001007737

• ChIP-seq of blasts from leukemia patients and CD34+ cells from healthy donors

  CTCF ChIP-seq of 14 leukemia patients: 6 AML without 3q rearrangements, 1 AML with 3q26, 1 AML with t(3;8) and 6 T-ALL H3K27ac ChIP-seq of AML patients: 4 cases with t(3;8), another with inv(3) and another with normal karyotype. H3K27ac ChIP-seq of CD34+ cells from one healthy donor RUNX1 ChIP-seq of one t(3;8) AML patient

  Dataset EGAD00001006817