Project description:The goal of this study was to gain insights into the transcriptomes, mutations and copy number variants present in small intestinal neuroendocrine tumors. The present dataset contains RNA-sequencing performed on seven such tumors.
Project description:Four cancer cell line, ie SW480-Vector, SW480-TET2, SW620-Vector and SW620-TET2 were treated with tgfb1, repsox and control. Then the total RNA of these samples were extracted and sequenced with Illumina Nextseq 500.
Project description:Total RNA was isolated from serum samples by the Qiagen miRNeasy Serum/Plasma extraction kit and QIAcube automation. All samples were quantified using the Nanodrop spectrophotometer prior to plating. Small RNA-seq libraries were prepared using the Norgen Biotek Small RNA Library Prep Kit and then sequenced on the Illumina NextSeq 500 platform at 51bp single end reads. ExceRpt was employed to assess the read quality and annotate miRNAs. The read count was log transformed and normalized by quantile normalization.
Project description:Inactivation of prospero in Drosophila neuroblasts during larval stages induces unlimited neuroblast amplification leading to tumors that persist growing in adults. Tumors present in the ventral nerve cord of adult flies were dissected, dissociated and GFP-labelled tumor neuroblasts were isolated by FACS. 10000 neuroblasts were then processed for single-cell RNA-seq analysis. Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina Nextseq 500. eLife 2019;8:e50375 DOI: 10.7554/eLife.50375
Project description:Small RNA (<100 bases in length) were purified from total RNA using miRNeasy kit (Qiagen), then sequenced. Libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq small RNA protocol (Illumina), starting from 1 µg of high quality total RNA. Single read (1 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on miRBase v.2052, then counted with STAR (v.2.5.2a). Counts were normalized with DESeq v1.30.0
Project description:Three cancer cell line, ie SW480, SW620 and Caco-2, were treated with TET2, TET2CD and control vector lentivirus. The expression of TET2 was validated using qPCR. Then the total RNA of these samples were extracted and sequenced with Illumina Nextseq 500.
Project description:Three libraries from 100 HEK293 cells each were prepared using a Smartseq based custom library preparation approach with unique molecular identifiers. Libraries were sequenced on a Illumina NextSeq 500
Project description:Total RNA was isolated from mouse Asxl2-/- and WT LK cells following standard protocol with TRIZol reagent (Life Technologies) followed by RNA library preparation with the Illumina TruSeq strand-specific mRNA sample preparation system. All RNA-seq libraries were sequenced with a read length of single-end 75bp using the Illumina NextSeq 500, and final of over 45 million reads per sample.
Project description:Purpose: Determine if alveolar macrophage express different transcriptional programs when CD44 expression is lost. Methods: Alveolar macrophages were isolated from the bronchoalveolar lavage of 6-10 week old CD44+/+ and CD44-/- female mice. RNA was isolated an sequenced using Illumina NextSeq 500. RNA was sequenced by the UBC Biomedical Research Center. RNA quality, 18S and 28S ribosomal RNA with RIN = 9.6, was determined by Agilent 2100 Bioanalyzer following standard protocol for NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 with paired end 42bp 42bp reads. De-multiplexed read sequences were then aligned to the Mus musculus (mm10) reference sequence using Spliced Transcripts Alignment to a Reference, STAR (https://www.ncbi.nlm.nih.gov/pubmed/23104886), aligners. Results and conclusion: Multiple pathways were abnormal in CD44-/- alveolar macrophages, in particular those involved in lipid metabolism and immune signaling.