Project description:This dataset contains spatial transcriptomics data of four lung neuroendocrine tumours (lung NETs), a rare and understudied type of lung cancer. The dataset consists of raw sequencing data, metadata, and gene expression matrices. It is part of the lungNENomics project. See https://doi.org/10.5281/zenodo.19366762 for processed data for the series, including downstream analyses data for the four samples in this dataset, such as inferred CNVs and aneuploidy status, and spatial domain and cell proportions for each spot. The lungNENomics project also generated other molecular data for a series of more than 200 samples. The raw sequencing data (fastq files for RNA-seq, cram files for WGS, and idat files for methylation arrays) is hosted on the European Genome-Phenome Archive website, study EGAS00001005979. Medical imaging data (Hematoxylin & Eosin stained whole-slide images) from the lungNENomics project is hosted in the EBI bioImage Archive (10.6019/S-BIAD3143).
Project description:This dataset contains bulk RNA sequencing data from paired aganglionic and ganglionic colonic tissue specimens obtained from three pediatric patients diagnosed with Hirschsprung disease (HSCR, OMIM 142623). RNA was extracted and sequenced to investigate transcriptomic alterations and signaling pathway dysregulation associated with HSCR pathogenesis. Raw paired-end FASTQ files generated by Illumina NovaSeq 6000 sequencing are provided for each sample, enabling downstream analyses of differential gene expression between diseased and unaffected intestinal segments.
Project description:This study describes the transcriptome of distinct blood compartments derived from whole blood collected from piglets. The dataset includes RNA-seq data from 20 samples representing five blood compartments: whole blood, serum, plasma, serum-derived exosomes, and plasma-derived exosomes. From each whole blood sample, the different fractions were carefully prepared using optimized and compartment-specific protocols. RNA-seq libraries were prepared using the LEXOGEN QuantSeq 3′ mRNA-Seq V2 Library Prep Kit with protocol adaptations for whole blood, plasma, serum, and exosome samples. Sequencing was performed on the Illumina NextSeq2000 platform in SR75. The 20 raw demultiplexed FASTQ files are part of this accession. Bioinformatic pre-processing was conducted using the Nextflow nf-core/rnaseq pipeline to ensure high sequence quality and robust transcriptome assembly and quantification. Each file contains raw sequencing reads along with base quality scores. Bioinformatic and statistical analyses explored the variability in gene detection and gene expression variability according to the five blood compartments.
Project description:This study investigates transcriptomic changes in human hepatocellular carcinoma (HCC) cell lines (Huh7 and HLF) cultured under different microenvironmental conditions, including 2D monolayer, 3D Inject-Embed, and 3D Mix-Embed cultures. RNA-seq was performed on total RNA using Illumina NovaSeq 6000 with paired-end 150 bp reads. Raw sequencing reads were aligned to the Homo sapiens reference genome (GRCh38/hg38) using STAR, and gene-level quantification was performed using featureCounts. The dataset includes raw FASTQ files and processed count and FPKM matrices for each sample. This resource provides insights into the impact of 3D culture on liver cancer gene expression.
