4732 results for "RNA AND sequencing OR transcriptome"

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

  RNA-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 EGAS50000001766

• RNA-seq analysis of midbrain dopaminergic neurons following ZFHX4 knockdown.

  We performed RNA-seq analysis on midbrain dopaminergic neurons derived from induced pluripotent stem cells following lentiviral-mediated knockdown of the transcription factor ZFHX4. Transcriptomic analysis enabled the identification of potential ZFHX4 target genes. Enrichment analysis of the differentially expressed genes was conducted to assess the biological pathways regulated by ZFHX4.

  Study EGAS50000001111

• Bell_activation_timecourse

  We purified human naive and memory B cells from PBMCs. We stimulated them with IgM cross-linker providing BCR stimulation, multimeric CD40L that engages costimulatory receptor CD40 on the B cell, and cytokines IL-2 and IL-21. To comprehensively characterise activation dynamics of naive and memory B cells, we performed single-cell RNA sequencing (scRNA-seq) and B cell receptor sequencing (BCR-seq) in resting cells (day 0), before the first division (day 1), at the time of the first division (day 3) and following the full B cell differentiation (day 6)

  Dataset EGAD50000002115

• Comprehensive single cell study of lung adenocarcinoma from early to metastatic stages

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes. The extensive single cell profiles depicted a complex cellular atlas and dynamics during lung adenocarcinoma progression which includes cancer, stromal, and immune cells in the surrounding tumor microenvironments.

  Dataset EGAD00001005054

• Dataset for synovial_sarcoma-RNA

  Rare cancer sequencing data of 23 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008844

• Bulk RNAseq of cancer-associated CD8 T cell populations

  Bulk mRNA sequencing of cancer-associated CD8 T cell populations isolated from tumor and tumor-adjacent tissue from non-small cell lung cancer patients. CD8 T cell populations isolated were CD103+CD39- and CD103+CD39+ from tumor tissue, and CD103+CD39- from adjacent tissue. These populations were isolated from 5 patients, totaling 15 samples. bulk poly-A RNA was isolated and libraries were prepped using the Smart-Seq2 protocol, followed by paired-end sequencing (Illumina). Raw data are in fastq format.

  Dataset EGAD50000002740

• Capture-based Methods for Transcriptomic Profiling of FFPE material

  This dataset includes all FASTQ files for 11 samples where different capture-based methods for transcriptome profiling have been tested. Specifically, we have the 'traditional' RNA-seq experiment with fresh frozen (FF) material, and 3 different capture methods for the matching formalin-fixed paraffin-embedded samples: Agilent (AGI), IDT, and Twist Biosciences (TBS). In total, there are 43 samples with paired-end FASTQ files (1 sample did not have sufficient material to test all methods). Samples are identified by the R01-R11 IDs with a suffix that indicates the capture method used (or FF for fresh frozen).

  Dataset EGAD00001007655

• Sequencing data for the manuscript "Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas"

  Mapping the spatial organization of DNA-level somatic copy number changes in tumors can provide insight to understanding higher-level molecular and cellular processes that drive pathogenesis. We describe an integrated framework of spatial transcriptomics, tumor/normal DNA sequencing, and bulk RNA sequencing to identify shared and distinct characteristics of an initial cohort of eleven gliomas of varied pathology and a replication cohort of six high-grade glioblastomas.

  Dataset EGAD50000001394

• scRNAseq of ALS patients

  The data set contains information from 9 individuals (5 ALS + 4 controls) using single cell RNA sequencing in combination with TCR V(D)J sequencing to study the immune profile of the central nervous compartment (CSF). Sequencing was done using 10x Genomics platform (5’ scRNAseq & V(D)J Reagent Kits v1.1). 5P and TCR libraries were then pooled and for sequencing on the NovaSeq sequencer. Provided files are in .fastq.gz format and per individual four files are available (Read 1&2 and Lane 1&2).

  Dataset EGAD00001009623

• Single-cell RNA-seq (10x) – melanoma samples

  This dataset comprises raw FASTQ files generated from single-cell RNA sequencing of metastatic melanoma lymph node samples using the 10x Genomics Chromium platform. Single-cell suspensions were prepared from tumour tissues, and libraries were constructed using 5′ or 3′ gene expression kits following the manufacturer’s protocol. Sequencing was performed on an Illumina platform to obtain high-throughput single-cell transcriptomic profiles. The dataset includes samples from patients with differing responses to immune checkpoint inhibitor therapy, enabling characterisation of tumour-resident immune cell populations and tumour–immune interactions associated with treatment response and resistance.

  Dataset EGAD50000002476