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| Status |
Public on Feb 10, 2015 |
| Title |
L55 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
gender: Female
treatment: TCDD
dose: 1
dose_unit: ug/kg
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| Treatment protocol |
Female ovariectomized C57BL/6 mice were gavaged daily with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 ug/kg TCDD every 4 days for 28 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were homogenized in TRIzol (Invitrogen, Carlsbad, CA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified and examined for purity and quality by nanodrop, Qubit, Bioanalyzer and visualization on a denaturing gel.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Mice dosed every 4 days for 28 days
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| Data processing |
Quality Control: FASTQC v0.11.2
Removal of adaptors and low-complexity reads: FASTX v0.0.14
Alignment: TopHat v1.4.1
Conversion to SAM format: SAMTools v0.1.19
Abundance measurement: HTSeq v0.6.1
Count transformation: DESeq
Normalization and analysis: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 74
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene
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| Submission date |
Oct 31, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Rance Nault |
| E-mail(s) |
naultran@msu.edu
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| Organization name |
Michigan State University
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| Department |
Institute for Integrative Toxicology
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| Street address |
1129 Farm Ln
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| City |
East Lansing |
| State/province |
United States |
| ZIP/Postal code |
48824 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE62902 |
RNA-Seq Versus Oligonucleotide Array Assessment of Dose-Dependent TCDD-elicited Hepatic Gene Expression in Mice [RNA-Seq] |
| GSE62903 |
RNA-Seq Versus Oligonucleotide Array Assessment of Dose-Dependent TCDD-elicited Hepatic Gene Expression in Mice |
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| Relations |
| BioSample |
SAMN03154428 |
| SRA |
SRX748973 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1535945_L55_count.txt.gz |
141.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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