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| Status |
Public on Mar 19, 2019 |
| Title |
1370-RP-62-GAGATTCC-CCTATCCT_S100 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: liver
time point: 5h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the liver, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA Mini Prep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
5h-vehicle
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| Data processing |
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files
Software tool Kallisto was used to generate Rnor_6.0 transcriptome index from ENSEMBL genome assembly release 92
Software tool Kallisto was used to obtain transcript abundances (units of Transcripts Per Million) in each sample with the Rnor6 transcriptome index generated in the previous step
Software tool Sleuth was used to assess differential expression of genes from the transcript abundances obtained using Kallisto
Genome_build: Rnor_6.0 ENSEMBL genome assembly release 92
Supplementary_files_format_and_content: The output of Kallisto for each sample, provided here as a .tar.gz archive, consists of a folder with the following contents: abundance.tsv (a text file that contains a total summary of transcript abundances), 100 bs_abundance_<i>.tsv files (i ranges from 0 to 99, each file is one bootstrap of transcript abundances), and run_info.json (a text file that contains information on the Kallisto run)
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| Submission date |
Dec 18, 2018 |
| Last update date |
Mar 19, 2019 |
| Contact name |
Kalyan C Vinnakota |
| E-mail(s) |
kalyan.vinnakota@gmail.com
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| Organization name |
Biotechnology HPC Software Applications Institute
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| Street address |
2405 Whittier Drive, Suite 200
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| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21788 |
| Country |
USA |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE124004 |
Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat: Liver Transcriptome Changes in Study 2 |
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| Relations |
| BioSample |
SAMN10606923 |
| SRA |
SRX5146715 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3518587_1370-RP-62-GAGATTCC-CCTATCCT_S100.tar.gz |
43.9 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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