Project description:Abstract: Paired-end sequence data has been generated using polyA selected RNA from a range of zebrafish tissues using the Illumina Genome Analyzer. Study description: Zebrafish total RNA was extracted from adult tissue, then polyA selected. After fragmentation and reverse transcription Illumina sequencing libraries were prepared. Paired-end sequence runs were performed with 76 base reads on the Illumina Genome Analyzer. ArrayExpress Release Date: 2011-01-28 Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute
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:Sheep total RNA was extracted from the Ileo-caecal valve lymph node (ICLN) of sheep with multibacillary paratuberculosis compared to ICLN of uninfected controls. Sequencing libaries were prepared from RNA using the Illumina TruSeq RNA Sample Preparation Kit v2. Sequencing with 101 base paired end reads was performed on an Illumina HiSeq 2500 at Edinburgh Genomics.
Project description:Although, there has been strong correlation between PNPLA3-I148M variants and metabolic dysfunction-associated steatotic liver disease (MASLD), the mechanism by which this variant drive the disease is not well understood. To this end, we perform this experiment to understand the transcriptomic changes that can be attributed to this variant. The total RNA was extracted from isolated primary human hepatocytes using RNeasy Plus Micro Kit (Qiagen). The sequencing library was constructed by following the Illumina Nextera XT Sample Preparation Guide. One nanogram of input cDNA was tagmented and amplified using the Illumina Nextera XT kit. Equimolar amounts of each sample were finally pooled and sequenced on an Illumina Nextseq 500 system, using a paired-end 75-bp strategy
Project description:The goal of scRNA-seq is to explore whether olfactory sensory neurons (OSNs) that display a specific olfactory receptor (OR) express a distinct transcriptional program from OSNs that display a different OR in a large and unbias scale. Olfactory epithelial single cell suspensions were made using 3 male and 3 female mice. Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) according to the manufacturer’s guidelines. Libraries were sequenced using 150 cycles of paired end reads on Illumina Hiseq4000 and Novaseq6000 instruments (Novogene). The sequencing reads were processed using the DolphinNext Single Cell-10X Genomics pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=420, default settings except STAR v2.6.1 was used for alignment).
Project description:We sought to explore the underlying mechanisms by which MCUR1 promotes erythropoiesis. Total RNAs were extracted from cultured human CD34+ HPCs stably expressing sh-MCUR1 or sh-Ctrl under hypoxia (1% O2) following 2 days of EPO stimulation, using TRIZOL Reagent (Invitrogen, CA, USA). RNA sequencing (RNA-seq) was performed using Illumina NovaSeq6000 at Berry Genomics Co. Ltd. (Beijing, China), and a mean of 40 million paired-end reads per sample was obtained.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Tuber magnatum truffles, free-living mycelium and oak mycorrhizal root tips. Paired-end reads of 100 bp were generated and aligned to Tuber magnatum reference transcripts using CLC Genomics Workbench 9.
Project description:Procedure: three independent experiments were done to generate three 96-well plates of E14-Tg2A gastruloids made with either homemade or commercial N2B27. 48 gastruloids per sample were used for RNA extraction using the Qiagen RNeasy Micro Kit. Library preparation and sequencing were done by the CRG Genomics Facility (Spain). Sequencing was done in a NextSeq 2000 and generated around 30M paired-end reads per sample.
Project description:Purpose: The aim of this study is to determine the absolute and relative expresson levels of mRNA transcripts across two purbred (Angus and Brahman) cattle and their receipicalcross. Methods: Total RNA was extracted and purified from five tissues using the RiboZero Gold kit. Sequencing libraries were prepared with a KAPA Stranded RNA-Seq Library Preparation Kit following the Illumina paired-end library preparation protocol. Completed libraries were sequenced on HiSeq 2000 as 100 bp paired-end reads at the Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Adelaide, Australia and USDA-ARS-US Meat Animal Research Center, Clay Center, USA. Approximately 60 million 100 bp single-end reads were obtained for each sample. Reads were aligned to the cattle reference genome UOA_brahman_1/UOA_angus_1 and mapped to known genomic features at the gene level using the Hisat2. Single reads were then summarized into gene-level counts using FeatureCounts.