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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 04, 2014 |
| Title |
Paired-end_AROM_rep3 |
| Sample type |
SRA |
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| Source name |
mammary glands
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| Organism |
Mus musculus |
| Characteristics |
gender: female
parity: nulliparous
strain: C57Bl/6
genotype: tet-op-CYP19A1MMTV-rtTA
tissue: mammary glands
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from homogenized mammary glands using Trizol (Invitrogen) and 300μl chloroform (Thermo Fisher Scientific, Waltham, MA) for phase separation, precipitated with 650μl isopropanol (Thermo Fisher Scientific) and purified using an RNeasy Plus Mini Kit (Qiagen, Valencia, CA).
Polyadenylated (polyA) RNA was isolated from 1ug total RNA and converted to cDNA using SuperScript II (Invitrogen). A TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) was used to generate sequencing libraries according to the manufacturer’s instructions. Libraries were independently sequenced by both single- and paired-end methods using HiSeq 2000 (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc), and contaminated adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/project/trim_galore).
Single- and paired-end reads of each biological replicate (single-end: two replicates of WT, Esr1, CYP19A1 and Brca1 KO; paired-end: one WT, two replicates of Brca1 KO and three replicates of Esr1 and CYP19A1) were aligned to the mouse reference genome (mm9 assembly) using TopHat.
Cufflinks was used to assemble transcriptomes, estimate the abundance of transcripts (FPKM, Fragments Per Kilobase of transcript per Million mapped reads) and identify differentially expressed genes (DEGs).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file reports FPKMs
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| Submission date |
Dec 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Keunsoo Kang |
| E-mail(s) |
[email protected]
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| Phone |
82-41-550-3456
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| Organization name |
Dankook University
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| Department |
Microbiology
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| Lab |
Computational Biology Lab
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| Street address |
Dandae-ro 119
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| City |
Cheonan |
| State/province |
Chungnam |
| ZIP/Postal code |
31116 |
| Country |
South Korea |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE63857 |
Comparison of tamoxifen and letrozole response in mammary preneoplasia of ER and aromatase over-expressing mice defines an immune-associated gene signature linked to tamoxifen resistance |
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| Relations |
| BioSample |
SAMN03252720 |
| SRA |
SRX796258 |
| 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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