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| Status |
Public on Oct 10, 2017 |
| Title |
Liver - Corn Oil KS3 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild type
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| Treatment protocol |
mRNA profiles of liver in adult male C57BL/6 mice treated with corn oil, PCN (mouse PXR-ligand), or TCPOBOP (mouse CAR ligand) were determined by RNA-Seq, n=3 per group, using an Illumina HiSeq 2000 sequencer.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNA zol Bee reagent (Tel Test Inc)
Illumina RNA-Seq library preparation
The complementary DNA (cDNA) libraries from total RNA samples were prepared by an Illumina TruSeq RNA sample prep kit (Illumina, San Diego, CA). Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer's protocol. The mRNAs were selected from the total RNAs by purifying the poly-A containing molecules using poly-T primers. The RNA fragmentation, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification were performed according to the manufacturer's protocol. The average size of the cDNA libraries was approximately 160 bp (excluding the adapters). The cDNA libraries were validated for RNA integrity and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) before sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
C57BL/6 wild type
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| Data processing |
using FastQC to check the quality of the reads
using Tophat to map the reads to the mouse mm10 genome
using Cufflinks to estimate the transcript abundance
Genome_build: mm10
Supplementary_files_format_and_content: Cufflinks output, can be open by excel
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| Submission date |
Oct 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Julia Yue Cui |
| E-mail(s) |
juliacui@uw.edu
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| Organization name |
University of Washington
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| Department |
Environmental and Occupational Health Sciences
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| Lab |
Cui
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| Street address |
4225 Rossevelt Way Ne
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE104734 |
RNA-Seq Profiling of Pharmacological Activation of PXR and CAR Mice |
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| Relations |
| BioSample |
SAMN07763412 |
| SRA |
SRX3262380 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2806878_cufflinks_output_KS3_CO3.zip.gz |
6.4 Mb |
(ftp)(http) |
ZIP |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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