ABSTRACT: BAM outputs from RSEM (https://deweylab.github.io/RSEM/) analysis of RNASeq sequencing on HiSeq platform of tumour samples from 29 pancreatic neuroendocrine cases.
Project description:BAM outputs from RSEM (https://deweylab.github.io/RSEM/) analysis of RNASeq sequencing on HiSeq platform of tumour samples from 95 pancreatic adenocarcinoma cases.
Project description:BAM outputs from STAR (https://github.com/alexdobin/STAR) analysis of RNASeq sequencing on HiSeq platform of 56 tumour samples from 46 melanoma cases.
Gene model = Ensembl version 70
Project description:We aimed to study the impact of bacteria-derived metabolites in solid organ transplantation. The short-chain fatty acid butyrate was administered using a new drug-delivery method developed by Wang et al. (https://doi.org/10.1038/s41551-022-00972-5). This system is based on a micelle platform that carries and protects butyrate (ButM) from degradation in the upper gastrointestinal tract, to lower distal portions of the gut. Mice (adult B6 females) were treated for 21 days with ButM (100mg/mL) or 1x PBS. Splenic Ly6Chi CD11b+ monocytes were sorted for bulk RNAseq using the Takara SMART-Seq mRNA LP and Unique Dual Index kits. Libraries were sequenced using the Illumina NovaSeq 6000 platform.
Project description:Purpose: We used RNA-seq to determine the mRNA species and cell types presented in the whole kidney tissue. Methods: We extracted RNA from the whole kidney tissue and microdissected proximal tubules. cDNA libraries were constructed for paired-end sequencing and sequenced on Illumina HiSeq3000 platform.Reads were mapped to mouse Ensembl Genome by STAR and transcript abundances were calculated in the units of transcripts per million (TPM) using RSEM (https://github.com/deweylab/RSEM). Results and conclusion: Based on a variety of data types we curated a list of 43 cell types that are thought to exist in the kidney. Our data indicated that, If mRNA levels parallel protein levels, the contribution of proximal tubules to total mRNA in the renal tubule is also likely to be in the vicinity of 66%.
Project description:Recently, we defined four subtypes of pancreatic cancer that are associated with distinct histopathological characteristics and differential survival, namely, Squamous, Pancreatic Progenitor, Immunogenic, and ADEX (Bailey et al 2016, Nature). We also found that loss of CXCR2 was associated with a switch away from the squamous subtype (Steele et al 2016, Cancer Cell). Here we set out to investigate whether inhibition of CSF1R could also result in an alteration of transcriptomic subtype. Pancreatic tumors were harvested from control KPC mice, or mice treated with CSF1R inhibitor (AZD7507) and/or CXCR2 inhibitor (AZD5069) (n≥5). Tissues were stored in RNAl8r at -80C before RNA was prepared, and RNASeq analysis carried out. Reads were analysed using the bcbio-nextgen framework (https://bcbio-nextgen.readthedocs.org/en/latest/). After quality control and adaptor trimming, reads were aligned to the mouse genome build (UCSC mouse mm10) using STAR. Counts for known genes were generated using the function featureCounts in the R/Bioconductor package Rsubread. The R/Bioconductor package edgeR was used to identify differentially expressed genes.
Project description:To investigate and delineate differences in the transcriptomic profiles of canine soft tissue sarcoma types, we ran RNAseq on 29 tumor samples.
