|
| Status |
Public on Mar 07, 2022 |
| Title |
STEMI_1_A |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood neutrophils
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripheral blood neutrophils
treatment: Unstimulated
disease state: STEMI
time: at presentation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human peripheral blood neutrophils were isolated by diluting peripheral venous blood collected in to EDTA tubes 1:1 with PBS and neutrophils were negatively enriched using the EasySep direct human neutrophil isolation kit as per the manufacturers instructions. Isolated neutrophils were with lysed with RLT (Qiagen) and stored at -80ºC. RNA was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
BAM to fastq file conversion using samtools v1.7 bam2fq.
Transcripts were quantified from reads using Salmon v1.2.1 with parameters --validateMappings --gcBias --seqBias -l A.
Counts were analysed using DESeq2 v1.24.0 / Bioconductor v3.8 / R v3.5.0. Transcripts with fewer than 10 counts across all samples were removed.
Variance stabilizing transformation was performed and normalized abundance values exported.
Genome_build: Ensembl 96 based on GRCh38
Supplementary_files_format_and_content: Comma-delimited matrix table with normalized abundance values for each sample and transcript
|
| |
|
| Submission date |
Nov 03, 2021 |
| Last update date |
Mar 07, 2022 |
| Contact name |
Robin Choudhury |
| Organization name |
University of Oxford
|
| Department |
Cardiovascular Medicine, Radcliffe Department of Medicine
|
| Lab |
Robin Choudhury
|
| Street address |
L6 West Wing, John Radcliffe Hospital, Headley Way
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE187571 |
RNA-sequencing of peripheral blood neutrophils from STEMI and NSTEMI patients at presentation and 1 month post-AMI |
|
| Relations |
| BioSample |
SAMN22866264 |
| SRA |
SRX12964375 |
