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Sample GSM3911304 Query DataSets for GSM3911304
Status Public on Jan 12, 2020
Title ctrl_52
Sample type SRA
 
Source name in vitro derived M2 macrophages
Organism Homo sapiens
Characteristics cell type: M2 macrophages
transfection: control
stimulation: non-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 SAMN12163120
SRA SRX6384182

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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