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Sample GSM6543612 Query DataSets for GSM6543612
Status Public on Oct 17, 2022
Title Surgical sample [M140S]
Sample type SRA
 
Source name breast cancer
Organism Homo sapiens
Characteristics tissue: breast cancer
treatment: Mifepristone neoadjuvant treatment
treatment response: Response
Treatment protocol Mifepristone tablets (200 mg) were purchased from Pharmaweb Canada (Montreal). Each patient received 1 pill of 200mg/day for 14 days by trained volunteers from La Liga Argentina de Lucha contra el Cáncer (Tigre) at the patient’s home signing forms to corroborate compliance. Surgery was performed on day 15.
Extracted molecule total RNA
Extraction protocol Frozen samples were pulverized and total RNAs were purified using TRIzol reagent (Life Technologies). RNAs were submitted to Macrogen, Inc (South Korea) for RNA sequencing.
SMART-SeqTM v4 UltraTM Low Input RNA Kit, TruSeq RNA Sample Prep Kit v2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The sequences were aligned to the Homo sapiens hg38 reference genome assembly using STAR. Downstream analysis was performed in R/Rstudio using Bioconductor packages.
The aligned data were counted using feature counts. Next, differentially expressed genes (DEG) were identified for pairwise comparison of CNB vs. surgery (pre- vs. post-treatment) using DESeq2.
Assembly: hg38 reference genome
Supplementary files format and content: tab-delimited text files include the normalized counts for each sample
 
Submission date Sep 04, 2022
Last update date Oct 17, 2022
Contact name Martin Carlos Abba
E-mail(s) mcabba@gmail.com
Phone 054-221-4236711
Organization name School of Medical Sciences - UNLP
Lab CINIBA
Street address 60 y 120
City La Plata
State/province Buenos Aires
ZIP/Postal code 1900
Country Argentina
 
Platform ID GPL24676
Series (1)
GSE212690 Beneficial effects of mifepristone treatment in breast cancer patients selected by the progesterone receptor isoform ratio: Results from the MIPRA trial
Relations
BioSample SAMN30671680
SRA SRX17424954

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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