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| Status |
Public on Nov 19, 2019 |
| Title |
Primary hepatocytes, Low, 24 h, MS-111 |
| Sample type |
SRA |
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| Source name |
Primary hepatocytes, Low (0.025 mM)
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley Rat
tissue: Liver
cell type: Primary hepatocytes
agent: thioacetamide-S-oxide
dose: Low (0.025 mM)
duration: 24 h
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| Growth protocol |
We cultured rat hepatocytes, renal cells, and cardiomyocytes for an additional 18 hours before adding thioacetamide-S-oxide or vehicle (maintenance medium; MM250 for hepatocytes and EpiCM for renal cells).
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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 double-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 |
Treatment
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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 Rattus norvegicus transcriptome (Rnor_6.0) downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o rat_Edik/"$sample" $DATA_DIR/3744-"$sample"_R1_001.fastq.gz $DATA_DIR/3744-"$sample"_R2_001.fastq.gz -t 10
Genome_build: Rattus norvegicus transcriptome (Rnor_6.0)
Supplementary_files_format_and_content: tab-delimited text files, including abundance measurements
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| Submission date |
Jul 19, 2019 |
| Last update date |
Nov 23, 2019 |
| Contact name |
Patric Schyman |
| E-mail(s) |
patric.schyman@gmail.com
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| Phone |
3016191978
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| Organization name |
Biotechnology HPC Software Applications Institute (BHSAI)
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| Street address |
2405 Whittier Drive, Suite 200
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| City |
Frederick |
| State/province |
Maryland |
| ZIP/Postal code |
21702 |
| Country |
USA |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE134569 |
In vitro transcriptomic responses to thioacetamide-S-oxide exposure in Sprague-Dawley rat primary hepatocytes, renal tube epithelial, and cardiomyocytes |
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| Relations |
| BioSample |
SAMN12323951 |
| SRA |
SRX6476562 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3956049_T.MS111_lll.txt.gz |
1009.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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