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 submission contains raw 10x Genomics Visium HD Spatial Gene Expression FASTQ files from three FFPE mucosa-associated lymphoid tissue lymphoma samples analyzed in the O2 marginal zone lymphoma study. Processed Space Ranger and downstream spatial transcriptomics files will be added before final GEO release. Submitter contact email: lcxujiadai@163.com.
Project description:To investigate the molecular effects of telomere damage in skeletal muscle by Terf2 knockout, we performed bulk RNA sequencing on gastrocnemius-plantaris-soleus (GPS) and tibialis anterior (TA) muscles isolated from Terf2 knockout (KO) and control (Cre) mice. Total RNA was extracted from dissected muscles and used for library preparation followed by paired-end sequencing. Samples include both male and female 8 month old mice. The dataset comprises biological replicates from KO and Cre genotypes for each muscle type. FASTQ files correspond to quality-filtered and trimmed reads used for alignment.
Project description:This dataset contains whole genome sequencing data, based in BAM files of three trio members. These BAM files contain information of chromsomes 21, X, Y and mitochondrial.
Project description:This dataset contains RNA-seq profiles from the posterior explants of Xenopus laevis embryos at stage 26. Explants were sectioned posterior to the otic vesicle and treated with 0.5 mM picrotoxin for 3 h to inhibit Gamma-Aminobutyric Acid (GABA) signaling, followed by removal of the ventral yolk. Two biological replicates were prepared for each condition, with each replicate pooling explants from three embryos. RNA-seq was performed to identify transcriptional changes associated with GABA signaling during tailbud-stage body axial elongation. The dataset includes raw FASTQ files and metadata, enabling the analysis of differential gene expression patterns under GABA inhibition.
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.
Project description:Sulforaphane (SFN) exhibits anticancer activity across diverse tumor models, yet its role under hypoxia—a hallmark of the colorectal cancer microenvironment—remains incompletely defined. In this study, colorectal cancer cells were cultured under hypoxic conditions and treated with SFN or a combination of SFN and 5-fluorouracil (5-FU). RNA-seq profiling was performed to characterize transcriptional alterations associated with SFN activity and SFN-mediated reversal of hypoxia-induced 5-FU resistance. The dataset includes paired-end raw FASTQ files, supporting further investigation into hypoxia-related signaling networks, including PI3K/AKT/mTOR and HIF-1α pathways.