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Sample GSM3984425

Query DataSets for GSM3984425

Status

Public on Jan 01, 2020

Title

2 hour replicate 1

Sample type

SRA

Source name

Whole brain

Organism

Bombina orientalis

Characteristics

tissue: Brain
post-training sacrifice timings: 2 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

2hour_vs_control.DESeq2.csv
eXpress_output
Annotation_File_Trinotate

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.
Read alignment was performed using Bowtie2 integrated in to the Trinity suite.
Differential expression analysis was performed using eXpress and DESeq2
Annotation was done using the Trinnotate annotation platform which uses the ref-seq NCBI, and Uniprot databases to run homology searches.
Gene ontology enrichment analysis and co-expression clustering was performed using the David Bioinformatics Resources website, and the MeV: MultiExperiment Viewer data analysis tool.
Supplementary_files_format_and_content: DESeq2 files for each treatment comparison (2h vs. con, 4h vs. con, 24 vs. con). Files are comma delimited and the output consists of log2 fold changes, p-values, and p-adjusted values (FDR).
Supplementary_files_format_and_content: eXpress output is a tab delimited file consisting of fpkm and tpm values for each transcript.
Supplementary_files_format_and_content: Full processed dataset is a tab delimited file which includes output from the trinotate annotation tool, abundance measure from the eXpress 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. TPM and FPKM are included for all transcripts, as well as , the log2 Fold-change and FDR for all differentially expressed transcripts.

Submission date

Jul 29, 2019

Last update date

Apr 09, 2021

Contact name

Vern Lewis

E-mail(s)

vernlewis@cunet.carleton.ca

Organization name

Carleton University

Department

Neuroscience