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| Status |
Public on Sep 30, 2017 |
| Title |
Estrogen (E2) control rep 2 |
| 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:
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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 |
SAMN07625351 |
| SRA |
SRX3172853 |
| 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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