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| Status |
Public on Apr 20, 2023 |
| Title |
RP-6 |
| 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 (duration after exposure): 5 h
agent: Vehicle
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from culture cells using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA MiniPrep 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 (New England BioLabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (KAPA Biosystems). Pooled libraries were subjected to 150-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Control
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| Data processing |
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the rat transcriptome (Rnor_6.0) downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o Rat/"$sample" $DATA_DIR/2516-"$p"_R1_001.fastq.gz $DATA_DIR/2516-"$p"_R2_001.fastq.gz -t 14
Genome_build: Rattus norvegicus Rnor6.0 Release 92
Supplementary_files_format_and_content: tab-delimited text files, including abundance measurements
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| Submission date |
Apr 17, 2020 |
| Last update date |
Apr 22, 2023 |
| Contact name |
Venkat R Pannala |
| E-mail(s) |
vpannala@bhsai.org
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| Phone |
+1 (301) 619-1976
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| Organization name |
Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc.
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| Department |
DoD BHSAI
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| Street address |
2405 Whittier Dr, #200
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| City |
Frederick |
| State/province |
Maryland |
| ZIP/Postal code |
21704 |
| Country |
USA |
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| Platform ID |
GPL25947 |
| Series (2) |
| GSE148852 |
In vivo transciptomic responses to bromobenzene exposure from liver and kidneys of Sprague Dawley rats |
| GSE148853 |
Mechanism-based identification of plasma metabolites associated with liver toxicity |
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| Relations |
| BioSample |
SAMN14612212 |
| SRA |
SRX8131233 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4484017_RP6.tsv.gz |
453.2 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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