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Series GSE111073 Query DataSets for GSE111073
Status Public on Mar 10, 2019
Title Expression profiling by RNA-Seq of breast cancer samples from patients in walnut-consuming and control groups
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Consumption of walnuts has slowed breast cancer growth and/or reduced the risk of breast cancer in mice. The significantly reduced mean tumor size or numbers of tumors was associated with changing the expressions of many genes that are associated with cancer growth, survival and metastasis. Many women treated for breast cancer are interested in reducing the risk for recurrence. The study was a non-placebo, two-arm, clinical trial. Women with lumps large enough for research and pathology biopsies were recruited to the trial. One or two additional biopsies were taken for gene expression analyses using next generation RNA Sequencing methods. The subjects randomized to the walnut group immediately began to consume 2 ounces of walnuts per day until follow-up surgery, if surgery were needed. At follow up surgery, additional biopsies were taken from the surgically removed, cancerous tissue for additional gene expression analyses. Changes in gene expression compared to baseline were determined in tumors of each individual woman in walnut-consuming and control groups.
 
Overall design Gene expression profiles of two samples from each of ten breast cancer patients were obtained via RNA-Seq in a 2x50bp paired-end design. The first sample was obtained from biopsy; the second sample was taken at the time of surgery 2-3 weeks later. Five patients consumed two one-ounce packets of walnuts daily between the biopsy and surgery, while the other five remained on their regular diet.
 
Contributor(s) Denvir J, Hardman WE, Primerano DA, Legenza MT, Morgan J, Fan J
Citation(s) 31198831, 30979659
W. Elaine Hardman, Donald A. Primerano, Mary T. Legenza, James Morgan, Jun Fan, James Denvir. Dietary walnut altered gene expressions related to tumor growth, survival, and metastasis in breast Cancer patients: A pilot clinical trial. Nutrition Research 2019. doi:10.1016/j.nutres.2019.03.004
Submission date Feb 23, 2018
Last update date Nov 19, 2019
Contact name James Denvir
E-mail(s) denvir@marshall.edu
Organization name Marshall University School of Medicine
Department Biochemistry and Microbiology
Lab Genomics and Bioinformatics Core Facility
Street address One John Marshall Drive
City Huntington
State/province WV
ZIP/Postal code 25755
Country USA
 
Platforms (1)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (21)
GSM3021588 109-biopsy-walnut-3-1
GSM3021589 109-surgery-walnut-3-1
GSM3021590 114-biopsy-walnut-4-1
Relations
BioProject PRJNA435751
SRA SRP133401

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE111073_normalized_counts.csv.gz 1.7 Mb (ftp)(http) CSV
GSE111073_pipeline.sh.txt.gz 1.7 Kb (ftp)(http) TXT
GSE111073_raw_counts.csv.gz 609.2 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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