2025-04-01
ENA first public
ERC000011
ENA-CHECKLIST
Latvian Biomedical Research and Study Centre
INSDC center name
public
INSDC status
ERS19315998
SRA accession
E-MTAB-14051:CB041-N
Submitter Id
ArrayExpress
broker name
not collected
collection date
human
common name
Protocols: Patients underwent BC surgery and tumour and adjacent normal tissue specimens were collected from the surgical material. Tissue specimens were macroscopically dissected by a histopathologist during surgery and stored in RNALater (Applied Biosystems, USA) at -20°C until processing. The “tumour bed” was marked before the NAC with 3-millimetre titanium metal clips to allow precise identification of the tumour site after the NAC. The tissue specimens were collected after the patient’s informed written consent was obtained. Approximately 45-50 mg of tissue were overlaid with 700 μl of QIAzol Lysis Reagent (Qiagen, USA) in Lysing Matrix A tubes (MP Biomedicals, USA), and homogenized twice for 40 seconds at 6 m/s using FastPrep-24™ device (MP Biomedicals). The tubes were centrifuged at 1000g for 10 min at +4°C and total RNA was extracted from the supernatant using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA was eluted in 30 μl of RNase-free water, quantified using NanoDrop 1000 (Thermo Ficher Scientific, USA) and the integrity of RNA was assessed with Agilent Bioanalyzer using RNA Nano chip (Agilent Technologies, USA). Total RNA samples (200 ng) were preprocessed to remove ribosomal RNA (rRNA) utilizing the MGIEasy rRNA Depletion Kit (MGI, China) and purified using RNA XP Cleanup Beads (Beckman Coulter, USA). RNA sequencing libraries were prepared using the MGIEasy RNA Directional Library Prep Set (MGI, China) according to the manufacturer’s instructions. The process involved fragmenting the RNA into approximately 250 bp fragments, reverse transcribing these fragments to create cDNA, and synthesizing the second DNA strand. Adapters were ligated to the synthesized DNA, which was subsequently amplified using PCR. The length and concentration of the PCR products were measured using an Agilent High Sensitivity DNA Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) and a Qubit fluorometer (Thermo Fisher Scientific, USA), respectively.
description
adult
developmental stage
breast cancer
disease
not collected
geographic location (country and/or sea)
CB041
individual
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
breast
organism part
Homo sapiens
scientific_name
female
sex
HIIT
stimulus
CB041-N
title
Normal
tumor grading