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Status |
Public on Jan 01, 2020 |
Title |
2 hour replicate 3 |
Sample type |
SRA |
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Source name |
Whole brain
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Organism |
Bombina orientalis |
Characteristics |
tissue: Brain post-training sacrifice timings: 2 hours post
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
2hour_vs_control.DESeq2.csv eXpress_output Annotation_File_Trinotate
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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.
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Submission date |
Jul 29, 2019 |
Last update date |
Apr 09, 2021 |
Contact name |
Vern Lewis |
E-mail(s) |
vernlewis@cunet.carleton.ca
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Organization name |
Carleton University
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Department |
Neuroscience
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Lab |
Dr. Argel Aguilar-Valles
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Street address |
1125 Colonel By Drive
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City |
Ottawa |
State/province |
Ontario |
ZIP/Postal code |
k1s5b6 |
Country |
Canada |
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Platform ID |
GPL26992 |
Series (1) |
GSE135054 |
Temporal profile of brain gene expression associated with learning in an anuran amphibian |
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Relations |
Reanalyzed by |
GSM5233623 |
BioSample |
SAMN12392377 |
SRA |
SRX6610631 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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