12214 results for "cancer rna-seq"

in 20.56 milliseconds.

• RNA-sequencing of SYSCOL colorectal adenoma-carcinoma samples

  RNA-sequencing alignment for SYSCOL colorectal adenoma-carcinoma samples

  Dataset EGAD00001003318

• HipSci - Monogenic Diabetes - RNA Sequencing - October 2016

  HipSci - Monogenic Diabetes - RNA Sequencing - October 2016

  Dataset EGAD00001003180

• HipSci - Monogenic Diabetes - RNA Sequencing - July 2017

  HipSci - Monogenic Diabetes - RNA Sequencing - July 2017

  Dataset EGAD00001003530

• HipSci - Bleeding and Platelet Disorders - RNA Sequencing - July 2017

  HipSci - Bleeding and Platelet Disorders - RNA Sequencing - July 2017

  Dataset EGAD00001003539

• HipSci - Healthy Normals - RNA Sequencing - May 2014

  HipSci - Healthy Normals - RNA Sequencing - May 2014

  Dataset EGAD00001000897

• Nanobody-Tethered Transposition Allows for Multifactorial Chromatin Profiling at Single-Cell Resolution

  Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility, and other factors. However, most current single-cell-resolution methods are unable to measure more than one aspect of chromatin state in a single experiment, limiting our ability to accurately measure chromatin states. Here we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), a new assay capable of measuring the genome-wide presence of multiple histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq utilizes recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk- and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and cells of the human immune system, demonstrating the high accuracy and sensitivity of the method. We further extend NTT-seq to enable simultaneous profiling of cell-surface protein expression alongside multimodal chromatin states to study cells of the immune system.

  Study phs003068

• Functional single-cell characterization of immune aplastic anemia shows convergence of NK and NK-like CD8+ T cells with disease-associated TCR signature

  Immune aplastic anemia (AA) is a life-threatening bone marrow (BM) failure disorder driven by an autoimmune T cell attack against the hematopoietic stem and progenitor cells (HSPCs). However, the autoantigen targets and the role of other immune cells are unknown. Here, by analyzing an international cohort of 156 AA patients with scRNA+TCRαβ-seq, TCRβ-seq, flow cytometry, and plasma cytokine profiling with comparisons to healthy controls and patients with other hematological disorders, we identify NK cells and CD8+ TEMRA cells expressing NK receptors with AA-associated TCRβ-seq motifs as the most dysregulated immune cell populations in AA BM. Functional co-culture experiments with scRNA-TCRαβ-seq readout utilizing primary HSPCs and immune cells provide evidence that NK cellscannot kill HSPCs alone, but sensitize them to CD8+ T cell-mediated killing. Furthermore, HSPCs induce strong activation of T cell clones with CD8+ TEMRA NK-like phenotype and AA-associated TCR motifs. Our results reveal the convergent evolution of innate and adaptive immune cells in AA, where NK cells support CD8+ T cell-mediated autoimmunity.

  Study EGAS00001007602

• Functional single-cell characterization of immune aplastic anemia shows convergence of NK and NK-like CD8+ T cells with disease-associated TCR signature

  Immune aplastic anemia (AA) is a life-threatening bone marrow (BM) failure disorder driven by an autoimmune T cell attack against the hematopoietic stem and progenitor cells (HSPCs). However, the autoantigen targets and the role of other immune cells are unknown. Here, by analyzing an international cohort of 156 AA patients with scRNA+TCRαβ-seq, TCRβ-seq, flow cytometry, and plasma cytokine profiling with comparisons to healthy controls and patients with other hematological disorders, we identify NK cells and CD8+ TEMRA cells expressing NK receptors with AA-associated TCRβ-seq motifs as the most dysregulated immune cell populations in AA BM. Functional co-culture experiments with scRNA-TCRαβ-seq readout utilizing primary HSPCs and immune cells provide evidence that NK cellscannot kill HSPCs alone, but sensitize them to CD8+ T cell-mediated killing. Furthermore, HSPCs induce strong activation of T cell clones with CD8+ TEMRA NK-like phenotype and AA-associated TCR motifs. Our results reveal the convergent evolution of innate and adaptive immune cells in AA, where NK cells support CD8+ T cell-mediated autoimmunity.

  Study EGAS00001007604

• The immunological characterization of expanded tumor-infiltrating lymphocytes in renal cell carcinoma patients

  In this study, we comprehensively characterized the non-expanded and expanded tumor-infiltrating lymphocytes (TILs) from treatment-naïve RCC patients, as well as the corresponding “young” TILs (pre-REP TILs) and “rapidly expanded” TILs (REP TILs) following a clinical-grade TIL production protocol. From our scRNA+TCRαβ-seq and TCRβ-seq analyses, we show that the REP protocol preferentially favors the expansion CD4+ T-cells that originate from small T-cell clones in the tumor microenvironment (TME), indicating that the large, exhausted T-cell clones in the tumor do not expand during the protocol. We further identified RCC-associated TCR motifs that were validated in multiple TCRαβ-seq and scRNA+TCRαβ-seq datasets, as well as quantified the RCC-associated TCRs from the REP protocol. Overall, the T-cells carrying the RCC-associated TCRs remained high in the tumors and corresponding pre-REP TILs, but the frequency was reduced in the REP TILs. Furthermore, the overall anti-viral TCRs remained low throughout the REP protocol. Our results provide an in-depth understanding of the origin, phenotype, and specificity of the TCRs in RCC TILs.

  Study EGAS00001006952

• Characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia

  RNA was extracted from eight diagnostic ETV6-RUNX1 positive acute lymphoblastic leukemia samples collected in PAXgene blood RNA tubes using PAXgene Blood RNA kit (cat #762174, Qiagen GmbH, Hilden, Germany), following the version 2 instructions for manual purification. Samples were processed with Globin-Zero Gold rRNA Removal Kit (Illumina) and directional libraries were prepared using NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs). The library preparation and paired end (150 bp) sequencing were performed by Novogene (HK) Company Limited (Hong Kong, China) using Illumina Novaseq 6000 aiming at 70 million read pairs per sample.

  Dataset EGAD00001006406

• Single-Cell Analysis of Human Adipogenesis

  The data in this study consists of RNA sequencing reads and read counts from single-cell and single-nuclei RNA sequencing experiments performed on two cell lines to investigate the transcriptional landscape of human adipogenesis in both the brown and white adipose tissue lineage. The two cell lines are human preadipocytes collected and isolated from a defined anatomical location in the neck of a single individual. This depot is known to harbor white adipose tissue (WAT) and brown adipose tissue (BAT). These white and brown preadipocytes were immortalized for the purposes of studying human adipogenesis in vitro. In this study we induced differentiation of these two preadipocyte lines and performed RNA sequencing on over 135,000 single cells spanning a 20-day time course from unperturbed preadipocytes to mature adipocytes from both brown and white lineages. Additionally, we performed both single-cell and single-nuclei RNA sequencing to comprehensively compare the advantages and disadvantages of either technique.

  Study phs002461

• Clear cell sarcoma sequencing data

  This study shares DNA and RNA sequencing data from Clear cell sarcoma patients

  Study EGAS00001006072

• HipSci - Bardet-Biedl Syndrome - RNA Sequencing - October 2016

  HipSci - Bardet-Biedl Syndrome - RNA Sequencing - October 2016

  Dataset EGAD00001003181

• HipSci - Bardet-Biedl Syndrome - RNA Sequencing - July 2017

  HipSci - Bardet-Biedl Syndrome - RNA Sequencing - July 2017

  Dataset EGAD00001003531

• RNA sequencing data to study "A biobank of patient-derived pediatric braintumor models"

  RNA sequencing data for the PDOX model EPD-613FH

  Dataset EGAD00001003573

• RNA sequencing of ALAL patients

  Transcriptomic data generated by RNA sequencing of 30 adults with acute leukemia of ambiguous lineage (ALAL)

  Dataset EGAD00001015547

• ATAC-seq in LCLs derived from constitutional MLH1 epimutation carriers and non-carrier relatives

  ATAC-seq performed in LCLs derived from constitutional MLH1 epimutation carriers and non-carrier relatives to profile alterations in chromatin accessibility associated with constitutional MLH1 epimutation.

  Dataset EGAD50000000714

• CIRCLE-seq of PDO

  CIRCLE-seq data of PDAC 1 patient-derived organoid (PDO) - Unmapped reads, libraries were sequenced using the Illumina NextSeq500 with the NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles), generating around 10M paired end 150bp reads per sample

  Dataset EGAD50000000281

• BLUEPRINT: WGBS-seq for monocytes and neutrophils

  WGBS-seq for monocytes and neutrophils

  Dataset EGAD00001000673

• McGill EMC Release 4 for assay "ATAC-seq"

  McGill EMC Release 4 for assay "ATAC-seq": Sequencing of transposase-accessible chromatin as described by Buenrostro et al. (Nature Methods 10, 1213?1218 (2013) doi:10.1038/nmeth.2688)

  Dataset EGAD00001001300

• single-cell ATAC-seq

  Single-cell ATAC-seq data for 5 CLL samples (2 controls, 3 tumor) of the CancerEpiSys-PRECiSe project.

  Dataset EGAD00001005965

• scDNA-seq

  Single cell DNA-seq data (CLL gene panel - Tapestri single-cell DNA CLL panel, Mission Bio)

  Dataset EGAD00001008960

• scRNA-seq of monocultures and co-cultures of PDAC-PDOs and CAFs

  scRNA-seq of monocultures and co-cultures of patient-derived PDAC organoids and matched CAFs. 3 sample sets per patient.

  Dataset EGAD00001009655

• Dataset for cancer_of_unknown_primary-RNA

  Rare cancer sequencing data of 58 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008857

• Dataset for breast_cancer-RNA

  Rare cancer sequencing data of 59 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008850

• Somatic L1 retrotransposition in normal colorectal epthelium

  Throughout an individual’s lifetime, genomic alterations accumulate in somatic cells. However, the mutational landscape induced by retrotransposition of long interspersed nuclear element-1 (L1), a widespread mobile element in the human genome, is poorly understood in normal cells. Here, we explored the whole-genome sequences of 406 normal colorectal clones, 12 MUTYH-associated adenomatous clones, and 19 matched colorectal cancer tissues. In addition, we analyzed promoter DNA methylation status of retrotransposition-competent L1 (in 139 clones) and read-through RNA expression profiles (in 116 clones) to investigate the epigenetic regulation of L1 activity.

  Dataset EGAD00001010183

• Whole-exome-sequencing and Whole-genome-sequencing and RNA-sequencing in Familial amyotrophic lateral sclerosis (ALS)

  To identify the genetic cause and modifiers of Familial amyotrophic lateral sclerosis (ALS), we performed Whole-exome-sequencing and Whole-genome-sequencing and RNA-sequencing of Familial amyotrophic lateral sclerosis (ALS) patients.

  Study JGAS000358

• Altered Blood and Keratinocyte microRNA/transfer RNA Fragment Profiles Related to Fibromyalgia Syndrome and its Severity

  We provide small RNA transcriptome signatures of whole blood and cultured keratinocytes, which separate FMS patients from healthy controls. This opens new perspectives for FMS diagnostics, symptom monitoring, and clinical management.

  Study EGAS50000000638

• Head and Neck Organoid Biobank cohort, Issing et. al., 2025, RNA + WES data

  This dataset contains the raw fastq files of RNA and whole exome sequencing of the head and neck organoid biobank. For RNA sequencing, 41 organoid samples collected at different timepoints as well as before and after genetic modification are included. For WES, 25 samples of early organoid cultures or matching tumor tissues are included.

  Dataset EGAD50000001733

• CANCAP03 single-nuclear RNA sequencing

  CANCAP03 single-nuclear RNA sequencing. Tissue punch cores for six patients, 3 from each of olaparib and olaparib and degarelix cohorts, were processed for nuclear isolation and extraction, prior to single-nuclear RNA sequencing. 10x libraries were constructed. Sequencing on NovaSeq 6000. FASTQ files were processed using CellRanger pipeline. Outputs from the CellRanger pipeline were analysed using the Seurat package in R.

  Dataset EGAD50000001280

• Dataset for Multiple Myeloma RNA data

  This dataset contains 371 case and control RNA sequencing samples of patients with multiple myeloma. Sequencing was performed on Illumina NovaSeq 6000 and HiSeq X, HiSeq 4000 and HiSeq 2000 using TruSeq Stranded RNA and TruSeq Stranded total mRNA Kits. The sequencing was always paired.

  Dataset EGAD50000000683

• RNA sequencing data of pediatric hypodiploid acute lymphoblastic leukemia

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one hypodiploid ALL patient (ALLT-351). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Ribo-Zero Magnetic Kit (Illumina) was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002605

• RNA Sequencing of Colorectal Liver Metastases

  Reverse-stranded paired-end 75 base-pair RNA sequencing libraries of 93 metastatic FFPE samples were constructed using Illumina Total RNA Stranded Kits. Ribosomal RNAs (rRNAs) were depleted by using the Ribo-Zero rRNA Removal Kit (Illumina). Libraries were sequenced on a HiSEQ2500 machine. Five samples were re-sequenced using paired-end 50 base-pair libraries due to the smaller insert sizes.

  Dataset EGAD00001004111

• Deep RNA sequencing in CLL

  Deep RNA sequencing in CLL

  Dataset EGAD00001000258

• HipSci - Healthy Normals - RNA Sequencing - May 2015

  HipSci - Healthy Normals - RNA Sequencing - May 2015

  Dataset EGAD00001001438

• TST170 Pilot RNA BAM

  TST170 Pilot RNA BAM files

  Dataset EGAD00001006044

• Two scRNA-seq datasets from control and irradiated organoids.

  Dataset includes two scRNA-seq samples from control and irradiated organoids. Files included in the dataset are Fastq files. Sample libraries produced with Chromium X were sequenced on an Illumina NovaSeq 6000 sequencer.

  Dataset EGAD50000001933

• Epigenetic profiles of neuroblastoma PDXs

  This dataset contains bam files for ChIP-seq experiments for 6 neuroblastoma PDXs (Patient Derived Xenograft). It includes the bam files for the H3K27ac mark as well as the bam files of the corresponding input DNA for each sample.

  Dataset EGAD00001003394

• BLUEPRINT: WGBS-seq of B cells

  Whole Genome Bisulfite-seq of four B cell samples

  Dataset EGAD00001000710

• BLUEPRINT September 2016, ATAC-seq for bone marrow, on Genome GRCh38

  ATAC-seq data for 4 sample(s) from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002710

• Results of scRNA-seq analysis of a PBMC collected from a male with a mosaic 45,X/48,XYYY karyotype

  Results of scRNA-seq analysis of a PBMC collected from a male with a mosaic 45,X/48,XYYY karyotype

  Dataset EGAD00001008645

• CLL ATAC Seq of Untreated and IBET762 treated samples

  CLL PBMC cells were isolated using ficoll gradient. They have been treated with IBET762 or DMSO as solvent control and ATAC Seq has been performed on them.

  Dataset EGAD00001008723

• Dataset to study clonal evolution in iAMP21 patient SJBALL021901 using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJBALL021901 with 71 high quality cells sequenced (67 blast and 4 normal)

  Dataset EGAD00001009755

• CITE-seq

  This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell CITE-seq Experiments, as well as the demultiplexed cell-donor identities matrices which were generated with Vireo (Analysis).

  Dataset EGAD00001009820

• Bolleboom-Gao peri-tumoral snRNA-seq glioblastoma dataset 2022/A

  Bolleboom-Gao peri-tumoral snRNA-seq glioblastoma dataset 2022/A

  Dataset EGAD00001009964

• ADARIO / Targeting ADAR1 in Immuno-Oncology

  RNA editing analyses of BRCA-isogenic cell lines and patient-derived xenografts (PDX)

  Study EGAS50000000518

• RNA-Sequencing and Somatic Mutation Status of Adrenocortical Tumors: Novel Pathogenetic Insights

  RNA paired end sequencing of 59 adrenocortical tumors and 4 controls.

  Dataset EGAD00001006258

• GTestimate: Improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator

  This study introduces a novel scRNA-seq normalization method, which takes unobserved genes into account. To validate GTestimate we designed a cell targeted amplification strategy, enabling us to sequence a small set of cells twice, once at a "typical" sequencing depth and once at a "ultra-deep" sequencing depth.

  Study EGAS50000000915

• 10X snRNA-seq data from human FCDII postoperative brain tissues with mTOR pathway mutations

  Focal cortical dysplasia type II (FCDII) is linked to mTOR pathway mutations and drug-resistant epilepsy. Using 10X snRNA-seq on postoperative FCDII brain tissues, we characterized transcriptional alterations across cell types, revealing mTOR-related dysregulation. These findings provide insights into FCDII pathology and potential therapeutic target

  Study EGAS50000000964

• ATAC-seq of iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimicking MPNST progression

  ATAC-seq data used in the paper "iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimics MPNST glial-to-neuro-mesenchymal transition and uncover new therapeutic opportunities" by Uriarte-Arrazola, 2026. The uploaded data was used to explore and validate the cellular model as an MPNST progression model.

  Study EGAS50000001764