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Status |
Public on Sep 30, 2017 |
Title |
0.2% γ-TmT rep 3 |
Sample type |
SRA |
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Source name |
Mammary tumor
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Organism |
Rattus norvegicus |
Characteristics |
strain: ACI tissue: Mammary tumor age: 40 weeks old
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Treatment protocol |
Rats are treated with 0.2% δ-T, 0.2% γ-T, 0.2% α-T, or 0.2% γ-TmT for 30 weeks
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Extracted molecule |
total RNA |
Extraction protocol |
Mammary tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
processed data file: E2_vs_gamma-TmT_gene_exp.diff
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Data processing |
Align fastq files to the reference genome (rn6) using tophat2 Assemble transcripts using cufflinks for each samples Run cuffmerge on all assemblies to create a single merged transcriptome annotation Run cuffdiff to compare experimental group to E2 control Genome_build: rn6 Supplementary_files_format_and_content: Diff file represting differentially gene genes, RPKM, p-value, q-value and significance from comparison of E2 control vs 0.2% δ-T, 0.2% γ-T, 0.2% α-T, or 0.2% γ-Tm
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Submission date |
Sep 08, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Nanjoo Suh |
E-mail(s) |
nsuh@pharmacy.rutgers.edu
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Organization name |
Rutgers University
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Street address |
164 Frelinghuysen Road
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City |
Piscataway |
State/province |
NJ |
ZIP/Postal code |
08854 |
Country |
USA |
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Platform ID |
GPL20084 |
Series (1) |
GSE103646 |
Differential gene regulation and tumor inhibitory activities of alpha-, delta- and gamma-tocopherols in estrogen-mediated mammary carcinogenesis |
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Relations |
BioSample |
SAMN07625376 |
SRA |
SRX3172858 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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