This readme.txt file was generated on <20241111> by Recommended citation for the data:К Arnold, SA, Low WC, Pluhar, GE. Breed-associated differences in differential gene expression following immunotherapy-based treatment of canine high-grade glioma *This manuscript will be submitted for publication to Animals once we have a link to a data repository, which is required for submission. Once the manuscript has been accepted for publication, we can update the citation. ------------------- GENERAL INFORMATION ------------------- 1. Title of DatasetК Transcriptomic data from RNA Sequencing of canine high grade glioma tumor samples 2. Author Information ККPrincipal Investigator Contact Information ККККККККName: Susan A. Arnold КККККККККККInstitution: University of Minnesota College of Veterinary Medicine КККККККККККAddress: 1352 Boyd Avenue, Saint Paul, MN 55108 КККККККККККEmail: saarnold@umn.edu К ORCID: 0000-0002-4081-1145 ККAssociate or Co-investigator Contact Information ККККККККName: G. Elizabeth Pluhar КККККККККККInstitution: University of Minnesota College of Veterinary Medicine КККККККККККAddress: 1352 Boyd Avenue, Saint Paul, MN 55108 КККККККККККEmail: pluha006@umn.edu К ORCID: 0000-0002-7881-5061 ККAssociate or Co-investigator Contact Information ККККККККName: Walter C. Low КККККККККККInstitution: University of Minnesota College of Medicine КККККККККККAddress: 2001 6th St SE, Rm 4-216, Minneapolis, MN 55455 КККККККККККEmail: lowwalt@umn.edu К ORCID:К 3. Date published or finalized for release:К 4. Date of data collection 20120101 to 20220101 5. Geographic location of data collection (where was data collected?): Saint Paul, MN 6. Information about funding sources that supported the collection of the data: Masonic Cancer Center ChildrenХs Cancer Research Fund 7. Overview of the data (abstract): These files contain the raw data for bulk RNA sequencing performed on canine high grade glioma tumor samples. These samples were obtained from three breeds of dogs: French bulldogs, boxers, and Boston terriers. All dogs were enrolled in immunotherapy clinical trials within the University of Minnesota Canine Brain Tumor Program. They were obtained from two different time points relative to treatment: pre-treatment and post-treatment. Treatment consisted of surgical resection and immunotherapy. The purpose of these data are to provide a comprehensive profile of how canine high grade glioma transcriptomes change in response to immunotherapy treatment, and to determine if there are breed-associated changes in differential gene expression. -------------------------- SHARING/ACCESS INFORMATION --------------------------К 1. Licenses/restrictions placed on the data: Creative Commons 2. Links to publications that cite or use the data: will update after manuscript publication 3. Was data derived from another source? КККККККККККIf yes, list source(s): No 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/policies/#drum-terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List КККA. Filename:К К French bulldog transcriptomes pre vs post treatmentКККК ККККККShort description:К This file contains gene expression data for French bulldogs pre versus post treatment. They are paired analyses.КККККК КККB. Filename: К Boxer and Boston terrier transcriptomes pre vs post treatmentККККК ККККККShort description:К This file contains gene expression data for boxers and Boston terriers pre versus post treatment. They are paired analyses.ККККККККККК 2. Relationship between files:КККККККК Both files contain gene expression data for dogs pre- and post-immunotherapy treatment -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Formalin-fixed, paraffin-embedded (FFPE) samples were used in this study. Two 10uM scrolls were cut from each paraffin block. RNA extraction and RNA sequencing (RNASeq) were performed at the University of Minnesota Genomics Center (UMGC). RNA was extracted and purified from scrolls using the PureLinkTM FFPE Total RNA Isolation Kit (Invitrogen, Carlsbad, CA). After elution of RNA, DNAse I digestion was performed to yield DNA-free total RNA. Total eukaryotic RNA isolates were quantified using a fluorimetric RiboGreen assay (Life Technologies, Carlsbad, CA). Total RNA integrity was assessed using capillary electrophoresis on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA), generating an RNA Integrity Number (RIN). A RIN cutoff of 2 was used for samples to be acceptable. Samples that passed quality control underwent library preparation using the SMARTer Stranded Total RNA-Seq Kit v2, Pico Input Mammalian (Takara Bio, Mountain View, CA); this kit removes ribosomal RNA. RNA sequencing was performed on the NovaSeq 6000 S1 flow cell, which produces 2 x 150 bp paired end reads (Illumina, San Diego, CA) at a targeted depth of і40 million reads per sample. 2. Methods for processing the data: RNASeq data were processed by the Minnesota Supercomputing Institute using PURR, a pipeline housed with the Collection of Hierarchical UMII/RIS Pipelines (CHURP). CHURP was developed by a group at the Minnesota Supercomputing Institute, and the analysis is provided as part of the RNASeq package run through the UMGC. Two x 50bp FastQ paired end reads for 29 samples (n=61.2 Million average reads per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional , Тheadcrop -3У option, Т-qУ option; 3bp sliding-window trimming from 3Х end requiring minimum Q30. Quality control on raw sequence data for each sample were performed with FastQC. Read mapping was performed via Hisat2 (v2.1.0) using the dog genome (Dog10K_Boxer_Tasha/canFam6 NCBI RefSeq assembly GCF_000002285.5) as reference. Gene quantification was done via Feature Counts for raw read counts. 3. Instrument- or software-specific information needed to interpret the data: R, R studio 4. Standards and calibration information, if appropriate: NA 5. Environmental/experimental conditions: HGO tissue samples were obtained from biopsy specimens submitted to the Comparative Pathology Shared Resource (CPSR) at the University of Minnesota College of Veterinary Medicine over a 10-year period from 2005 to 2015. Samples from a total of 18 dogs diagnosed with HGO were included. The samples used in this report were obtained via surgical resection as part of enrollment in clinical trials for pet dogs with high grade gliomas. All samples were obtained prior to trial treatment. These studies were approved by the University of Minnesota Institutional Animal Care and Use Committee (IACUC; protocols 2001-37742A, 2002-37886A, 2111-39571A, and 2111-39569A). Biopsy specimens were submitted to CPSR in 10% neutral buffered formalin and were then embedded in paraffin wax. Hematoxylin and eosin (H&E) stain sections were reviewed by a board-certified veterinary pathologist to confirm a diagnosis of HGO in all cases based on criteria described in the WHO Classification of Tumors of the Central Nervous System. 6. Describe any quality-assurance procedures performed on the data: Total RNA integrity was assessed using capillary electrophoresis on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA), generating an RNA Integrity Number (RIN). A RIN cutoff of 2 was used for samples to be acceptable. 7. People involved with sample collection, processing, analysis and/or submission: Susan A. Arnold, G. Elizabeth Pluhar, Juan E. Abrahante Llorens, UMGC, MSI ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [FILENAME] ----------------------------------------- 1. Number of variables: 1 2. Number of cases/rows: 18 3. Missing data codes: ККККККККCode/symbolК К К К Definition ККККККККCode/symbolК К К К Definition 4. Variable List КККККККККККККККККК ККККA. Name: КККККККDescription: ККККККККККККККККККККValue labels if appropriate