Project description:This RNA-seq dataset contains whole blood transcriptome profiles from individuals with X-linked familial Kallmann syndrome associated with a new variant in the ANOS1 gene (c.452G>C). Samples were collected from two affected male siblings, their mother, and controls. Total RNA was extracted from whole blood, and ribosomal RNA was depleted prior to library preparation using the KAPA RNA HyperPrep Kit with RiboErase. Paired-end RNA sequencing was performed on the Illumina NovaSeq X Plus platform, generating approximately 100 million paired-end reads per sample. Sequencing utilized 1% of a 10B, 300-cycle flow cell, which produces up to 20 billion paired-end reads per flow cell. This dataset enables a comprehensive analysis of gene expression and splicing patterns associated with ANOS1-related Kallmann syndrome, providing a valuable resource for studying transcriptomic alterations in hypogonadotropic hypogonadism.
Project description:Intrahepatic cholangiocarcinoma (iCCA) is a fatal bile duct cancer with dismal prognosis and limited therapeutic options. By performing RNA- and exome sequencing analyses we have discovered a novel fusion event, FGFR2-PPHLN1 (16%), and damaging mutations in the ARAF oncogene (11%). Methods: mRNA and gDNA were exctracted from fresh frozen tumor tissues and corresponding normal tissue (n=8 pairs) from patients with iCCA who underwent surgical resection. RNA-seq was performed using Illumina HiSeq 2500 System with 100 nucleotide single-end reads. One sample and its paired non-tumoral tissue were eliminated from the subsequent analysis because of bad RNa quality. The same 8 paired tumors were also analyzed by whole-exome seq. Submitter confirms there are no patient privacy concerns with these data. This dataset is part of the TransQST collection.
Project description:This dataset contains bulk RNA-seq profiles of HONE-1 nasopharyngeal carcinoma cells transfected with negative control siRNA or siRNA targeting FBXO8. Three biological replicates were included in each group. Total RNA was extracted for paired-end RNA sequencing to investigate transcriptional changes associated with FBXO8 knockdown in nasopharyngeal carcinoma cells.
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:Dataset contains paired-end Whole Exome sequencing data from 257 glioma samples from 28 patients. 26 normal blood samples are also included.
Project description:Histologically normal human breast FFPE specimens were profiled by NanoString nCounter to study parity-conditioned basal/progenitor, Hedgehog, and vitamin D receptor-associated biology in normal breast tissue. This workbook contains the Breast Cancer 360 (BC360) arm of the study and is paired with a companion workbook for the other NanoString panel. Each of the 74 analyzed specimens contributes one GEO sample to this platform-specific workbook and one GEO sample to the companion panel workbook.
Project description:Histologically normal human breast FFPE specimens were profiled by NanoString nCounter to study parity-conditioned basal/progenitor, Hedgehog, and vitamin D receptor-associated biology in normal breast tissue. This workbook contains the PanCancer IO 360 (IO360) arm of the study and is paired with a companion workbook for the other NanoString panel. Each of the 74 analyzed specimens contributes one GEO sample to this platform-specific workbook and one GEO sample to the companion panel workbook.
Project description:scRNAseq of chicken basilar papilla at P7 and P11 as controls, and 12, 16, 20, 24, 30, 38, 48, and 96 hours post sisomicin administration. Cells were isolated using FACS and underwent Smartseq-2 protocol for single cell RNA seq with paired-end sequencing. Processed data file contains SingleCellExperiment object with all metadata. The dataset has undergone quality control using scater package in R, normalized using SCnorm, and normalized counts were log2 transformed (found in RDS file here). Only genes expressed in at least 3 cells are included for a total of 16,302 genes. A total of 2,625 high quality cells are in the normalized dataset. Raw sequence data for all 3,831 sequenced cells pre-quality control is also included.