11769 results for "cancer rna-seq"

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• scRNA-seq dataset of A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories

  Study describing the differentiation trajectory...

  Dataset EGAD00001015545

• RNA sequencing of SCLC tumor/normal sample pairs and cell lines

  RNA sequencing of SCLC tumor/normal sample pairs and cell lines

  Dataset EGAD00001000223

• Impact of BRCA mutation type in non-tumorous breast tissue transcriptome

  To investigate the transcriptomic difference between BRCA1 vs. BRCA2 carriers, RNA sequencing was carried out.

  Study EGAS00001004890

• RNAseq cutaneous and uveal melanoma liver metastases

  RNA sequencing analyses of tumor liver metastases from untreated cutaneous melanoma (CM) and uveal melanoma (UM) patients.

  Study EGAS00001004794

• Total RNA sequencing in M1911

  The dataset comprises total RNA sequencing data obtained from two samples of testicular tissue from the individual M1911, who was diagnosed with meiotic arrest.

  Dataset EGAD00001008639

• Plasma RNA sequencing

  Plasma RNA sequencing (consists of 70 cases)

  Dataset EGAD00001008836

• RNA Sequencing of paediatric patients with B lymphoblastic leukemia

  RNA sequencing was performed on 54 bone marrow samples at diagnosis of paediatric patients with B lymphoblastic leukemia.

  Dataset EGAD00001005103

• RNA sequencing of AD, MCI and control OM cells

  Total RNA sequencing of cultured OM cells derived from patients with Alzheimer's disease (AD), individuals with mild cognitive impairment (MCI) and cognitively healthy controls.

  Dataset EGAD00001008707

• RNA sequencing of human ILC3 from lymphoid organs and blood

  Rna sequencing of purified human group 3 innate lymphoid cells from non-reactive lymph nodes and spleen, inflamed tonsils and peripheral blood.

  Dataset EGAD00001003704

• Dataset for RNA PCNSL

  RNA sequencing of 19 samples from PCNSL tumors. Sequencing was performed on a HiSeq X Ten using Illumina TruSeq Stranded mRNA Kit. Sequencing was always paired.

  Dataset EGAD00001011119

• Single-cell RNA and TCR sequencing of 40 advanced HCC biopsies.

  Single-cell RNA and TCR sequencing of 40 advanced HCC pre-treatment biopsies from 38 patients.

  Dataset EGAD00001011347

• Exome and RNA sequencing data from 32 ocular and extraocular sebaceous carcinomas

  Sebaceous carcinomas (SeC) are cutaneous malignancies that, in rare cases, metastasize and prove fatal. Here we report whole exome sequencing on 32 SeC, revealing distinct mutational classes that explain both cancer ontogeny and clinical course. A UV-damage signature predominated 10/32 samples, while 9 were instead defined by microsatellite instability (MSI) mutations. UV-damage SeC exhibited poorly differentiated, infiltrative histopathologycompared to MSI signature SeC (p = 0.003), features previously associated with dissemination. Strikingly, UV-damage SeC transcriptomes and anatomic distributionclosely resembling those of cutaneous squamous cell carcinomas (SCC), implicating sun-exposed keratinocytes as a cell of origin. Like SCC, this UV-damage subclass harbors a high somatic mutation burden with >50 mutations/Mb, predicting immunotherapeutic response. In contrast, ocular SeC acquire far fewer mutations without a dominant signature, but show frequent truncating mutations in the ZNF750 epidermal differentiation regulator. Our data exemplify how different mutational processes convergently drive histopathologically related but clinically distinct cancers.

  Study EGAS00001002869

• Whole Exome sequencing of colorectal cancer patients (SG-BULK)

  DNA-seq libraries were captured to exome regions using xGen Exome Research Panel v1.0 (IDT), and libraries were prepared using the KAPA Hyper prep kit. DNA libraries were sequenced to a target depth of ×200 for tumor sample, ×100 for normal samples on the Illumina HiSeq platform.

  Dataset EGAD00001008543

• Linking the epigenetic landscape in chronic lymphocytic leukemia to deregulated chromatin networks

  Aberrant chromatin features and epigenetic signaling emerge as an important part of the tumor disease state in chronic lymphocytic leukemia (CLL). However, an integrative analysis of the malignant chromatin landscape is currently missing. Here, we mapped DNA-methylation, nucleosome position, 7 histone modifications, ATAC-seq and the transcriptome in primary CD19+ sorted B-cells from the peripheral blood of CLL patients in comparison to non-malignant lymphocytes of healthy donor reference samples. On the > 50 kb scale we identified global differences with respect to DNA methylation, nucleosome positioning and histone modifications in CLL. Furthermore, a chromatin state annotation was developed to identify deregulated chromatin features of promoters and enhancers in CLL. By integrating these findings with an ATAC-seq based transcription factor binding analysis we identified a set of promoters and enhancers specific to CLL that were enriched in certain transcription factors binding motifs and genes of the BCR signaling pathway. Thus, our study provides an in-depth map of the CLL chromatin landscape and links chromatin state changes at promoters and enhancers to deregulated pathways.

  Study EGAS00001002518

• A Single-cell Atlas of Progressive TKI Resistance in Chronic Myeloid Leukemia

  High-dimensional scRNA seq and CyTOF were used to identify features predictive of treatment outcome at diagnosis. An optimal TKI response was characterised by erythroid lineage skewing of the CD34+ HSPC compartment. While TKI-resistant CP was reminiscent of a BC-like state, where HSPCs were enriched for inflammation, stemness and quiescence. We designed a machine-learning approach which assessed the prognostic potential of all 32 sub-populations of our scRNA seq dataset. LSCs and NK populations harboured the highest prognostic power at diagnosis. Within the LSCs, erythroid lineage priming and MYC activation were features of an optimal and poor TKI responses, respectively. With the NK cell compartment, apart from a higher abundance of NK cells in TKI optimal responders, a memory-like HLA-DR+ adaptive NK and KLRC1+ NK populations were hallmarks of an optimal and poor TKI responses, respectively. Mechanistically, both cell intrinsic and extrinsic mechanisms contributed towards the higher sensitivity of EPs to TKI therapy. In summary, our high-dimensional single-cell atlas of TKI resistance highlights pivotal transcriptional features associated with TKI-resistance disease, some of which have the potential to be exploited as biomarkers.

  Study EGAS00001005509

• Rheumatoid Arthritis Finger Stick RNA Sequence Data

  This is a longitudinal study of 355 blood samples collected weekly from 5 patients with Rheumatoid Arthritis with varying disease activity over the course of one to five years. Blood samples were self collected from finger sticks and mailed from home. RNA was extracted, purified and sequenced.

  Study phs003179

• RNA-sequencing of 82 pleural mesothelioma samples

  The dataset contains RNA-sequencing data (bam files) for 82 pleural mesothelioma samples. All the samples were sequenced on an Illumina NovaSeq 600 sequencer in paired-end mode, generating 100 nt length reads, to obtain an average of 60 million clusters for RNA. Demultiplexing was performed using Illumina bcl2fastq2. Fastq quality was assessed using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and low-quality reads were discarded. Sequence reads were aligned to Human reference genome (UCSC genome assembly GRCh38/hg38) using STAR (v. 2.7.0b).

  Dataset EGAD50000002131

• RNA sequencing of BCP-LBL and EM B-ALL patients samples

  In order to perform comprehensive transcriptomics and gene fusion analyses of a cohort of BCP-LBL and extramedullary (EM) manifestations of B-ALL patients, we performed RNA sequencing of 16 tissue samples from BCP-LBL and EM B-ALL 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 EGAD50000002047

• 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

• Single-cell RNA-sequencing of rhabdomyosarcoma tumouroids (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell RNA sequencing of RMS tumouroids data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015708

• Bulk RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the bulk RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015714

• Bulk RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the bulk RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015718

• small RNA sequencing for 6 patients

  small RNA sequencing data for 3 patients with type 2D diabetes, and 3 patients with non diabetes. Single end sequencing was performed with read length of 100.

  Dataset EGAD50000001259

• Dataset of single cell RNA sequencing of peripheral blood HSPC

  Here, we conducted peripheral blood CD34+ cells single-cell RNA sequencing of patients with sickle cell anemia (n=4) and healthy donors (n=3)

  Dataset EGAD50000001522

• Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population

  We mapped microRNA expression quantitative trait loci by quantifying microRNA expression using small RNA sequencing.

  Study JGAS000504