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Status |
Public on Aug 01, 2021 |
Title |
2 hour rep 2 |
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 |
Extinction_VS_Acquisition_Analysis Ext_vs_Acq_2h_DESeq2.csv
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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. 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.
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Submission date |
Apr 09, 2021 |
Last update date |
Aug 01, 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) |
GSE171766 |
Temporal profile of brain gene expression associated with learning in an anuran amphibian II |
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Relations |
Reanalysis of |
GSM3984426 |
BioSample |
SAMN18680965 |
SRA |
SRX10562581 |
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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