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Sample GSM5233626

Query DataSets for GSM5233626

Status

Public on Aug 01, 2021

Title

24 hour rep 3

Sample type

SRA

Source name

Whole brain

Organism

Bombina orientalis

Characteristics

tissue: Brain
post-training sacrifice timings: 24 hours post

Extracted molecule

polyA RNA

Extraction protocol

Trizol extraction + isolation with a Qiagen RNease kit
RNA libraries were prepared for sequencing using standard Illumina protocols by The Center for Advanced Genomic (TCAG) at The Hospital for Sick Children's.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

Extinction_VS_Acquisition_Analysis
Ext_vs_Acq_24h_DESeq2.csv

Data processing

RNA-seq was performed on RNA extracted from Brain tissue.
Quality trimming and de novo transcriptome assembly was performed using the Trinity assembly suite. Current samples were combined with 2h & 24h samples from previous GEO submission: GSE135054.
Read alignment was performed using Bowtie2 integrated in to the Trinity suite.
Differential expression analysis was performed using RSEM and DESeq2
Annotation was done using the Trinotate annotation platform which uses the ref-seq NCBI, and Uniprot databases to run homology searches.
Gene ontology and pathway enrichment analysis was performed using the David Bioinformatics Resources website, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.
Supplementary_files_format_and_content: Differential expression measure: DESeq2 files for each treatment comparison (Extinction 2h vs. Acquisition 2h, Extinction 24h vs. Acquisition 24h, Long-trained 2h vs. Short-trained 2h, Long-trained 24h vs. Short-trained 24h). Files are comma delimited and the output consists of log2 fold changes, p-values, and p-adjusted values (FDR).
Supplementary_files_format_and_content: Filtered processed data file for each analysis (Extinction vs. Acquisition & Long-trained vs. Short-Trained). Each file includes the log2 fold change, FDR, and annotation information for all DEG in each analysis. These files contain the final processed datasets used in the publication.
Supplementary_files_format_and_content: Full processed dataset is a tab delimited file which includes the unfiltered output from the Trinotate annotation tool, abundance measure from the RSEM tool, and differential expression output from DSeq2. Trinotate output consists of homology search results from both NCBI's refseq database and Uniprots protein database. Also included are pfam, signalP, eggnog, KEGG, and gene ontology annotations, as well as the associated nucleotide and protein sequences. The log2 Fold-change and FDR for all differentially expressed transcripts are included.
Supplementary_files_format_and_content: Assembled Transcriptome file contains all de novo assembled transcripts from the Trinity tool.

Submission date

Apr 09, 2021

Last update date

Aug 01, 2021

Contact name

Vern Lewis

E-mail(s)

vernlewis@cunet.carleton.ca

Organization name

Carleton University

Department

Neuroscience