|
Status |
Public on Oct 17, 2022 |
Title |
Core needle biopsy [M140B] |
Sample type |
SRA |
|
|
Source name |
breast cancer
|
Organism |
Homo sapiens |
Characteristics |
tissue: breast cancer treatment: Control 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 |
SAMN30671681 |
SRA |
SRX17424953 |