2025-08-31
ENA first public
ERC000011
ENA-CHECKLIST
Department of Translational Genomics, GROW – Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
INSDC center name
public
INSDC status
ERS21368677
SRA accession
E-MTAB-14563:Sample 172
Submitter Id
ArrayExpress
broker name
not collected
collection date
human
common name
Protocols: Whole blood samples were collected from participants using standard venipuncture techniques into EDTA-coated tubes during specific test days. On the collection day, participants arrived at the research facility after fasting overnight. Immediately after blood collection, the samples were transferred into freezer-safe Eppendorf tubes containing RNAlater solution (Ambion, Austin, TX, USA) in a 2:1 ratio (RNAlater to blood volume). This step was taken to stabilize the RNA in the samples. The tubes were then stored at -80°C until further processing. The samples were collected both at baseline and post-intervention phases, ensuring uniform handling across all time points. RNA extraction from the blood samples was performed using the Directzol RNA microprep kit (ZY-R2052, Zymo Research), following the manufacturer's protocol. Before extraction, the blood samples were thawed on ice, and the RNAlater solution was removed by centrifugation at 5000× g for 1 minute. After the supernatant was discarded, 1xPBS (phosphate-buffered saline) was added to wash the pellet, followed by centrifugation to remove remaining impurities. QIAzol lysis reagent (QIAGEN) was then added at a 3:1 ratio, and the mixture was vortexed to ensure thorough lysis. Chloroform was added for phase separation, and the samples were centrifuged at 1200× g for 15 minutes at 4°C. The RNA-containing aqueous phase was transferred to a new tube, mixed with ethanol, and processed using Directzol spin columns. The extracted RNA was eluted in RNase-free water, and RNA quality and concentration were measured using a Qubit Fluorometer (Life Technologies) and a Bioanalyzer (Agilent Technologies). Only samples with RIN (RNA Integrity Number) greater than 7 were used for further analysis. RNA libraries were prepared using the NextFlex Rapid Directional RNA kit 2.0 with ribo-depletion (Perkin Elmer, Waltham, MA, USA). Approximately 100 ng of total RNA was used for each library preparation, with ribo-depletion carried out to remove rRNA. The libraries were constructed following the manufacturer's guidelines and were normalized according to RNA concentration and library size. The prepared libraries were checked for quality and fragment size distribution using a Bioanalyzer (Agilent Technologies).
description
2
diet
not collected
geographic location (country and/or sea)
64
individual
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
blood
organism part
Homo sapiens
scientific_name
Sample 172
title