|
Status |
Public on Jan 12, 2020 |
Title |
ctrl_LPS_95 |
Sample type |
SRA |
|
|
Source name |
in vitro derived M2 macrophages
|
Organism |
Homo sapiens |
Characteristics |
cell type: M2 macrophages transfection: control stimulation: LPS-stimulated
|
Treatment protocol |
miR-221-3p mimic was added 63.5 hours prior to stimulation with 100 ng/ml LPS for 8.5 hours.
|
Growth protocol |
M2-macrophages from 5 HD were cultured in 12 well plates with 540’000 cells/well.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA for the 20 resulting samples was isolated using miRNeasy Micro kit (Qiagen). RNA quality was assessed with a Fragment Analyzer (Advanced Analytical). Library preparation was performed using the Illumina Truseq stranded kit.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Single-end 81-mers reads were obtained and their quality was assessed with the FastQC tool (version 0.11.3). Reads were mapped to the human hg38 genome assembly with STAR (version 2.5.2a_modified) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”). Gene expression was quantified by the qCount function of the R Bioconductor package QuasR (version 1.18) as the number of reads that started within any annotated exon of a gene from the UCSC knownGenes annotation (downloaded on 2017-04-03). Genome_build: hg38 Supplementary_files_format_and_content: gzipped text file with tab-separated counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. Entrez Gene ID, 2. gene length (exon union model), 3.-22. read counts per gene and sample.
|
|
|
Submission date |
Jun 28, 2019 |
Last update date |
Jan 12, 2020 |
Contact name |
Diego Kyburz |
E-mail(s) |
diego.kyburz@usb.ch
|
Organization name |
University of Basel
|
Department |
Biomedicine
|
Lab |
Experimental rheumatology
|
Street address |
Petersplatz 4
|
City |
Basel |
ZIP/Postal code |
4031 |
Country |
Switzerland |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE133527 |
miR-221-3p drives the Shift of M2-Macrophage to a Pro-Inflammatory Function by Modulating JAK3/STAT3 Signaling and is Increased in Rheumatoid Arthritis |
|
Relations |
BioSample |
SAMN12163112 |
SRA |
SRX6384190 |