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Sample GSM3734143 Query DataSets for GSM3734143
Status Public on Apr 01, 2021
Title MitoStress stimulated cells rep3
Sample type SRA
 
Source name human umbilical vein endothelial cells (HUVEC)
Organism Homo sapiens
Characteristics cell type: human umbilical vein endothelial cells (HUVEC)
Treatment protocol Cells were stimulated for 6 hours with MitoCo or MitoStress for 6 hours in FBS-free EBM-2 media.
Growth protocol HUVECs were grown in complete EBM-2 media (Lonza)
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated by using Rneasy Mini Kit (Qiagen)
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using 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 acquistion on the sequencing instrument.
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing was performed with Illumina2bam tools 1.17 (https://github.com/wtsi-npg/illumina2bam)
The transcriptome analysis was performed using the Tuxedo suite. TopHat2 (v2.1.1, http://genomebiology.com/2013/14/4/R36/abstract) was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e87, December 2016) as reference. TopHat2 analyses were run independently for each replicate.
Cufflinks (v2.2.1, http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) was then used to assemble transcripts from spliced read alignments, again using the Ensembl e87 transcriptome as the reference, allowing also de novo assembly of transcript models.
Transcriptome sets of all replicates for each sample group were combined with Cuffmerge.
Differential expression was assessed with Cuffdiff v2.2.1 (http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html).
cummeRbund (http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html) and biomaRt (http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html) were used in combination with custom R scripts to perform quality assessment and further refine analysis results.
Genome_build: GRCh38 (UCSC hg38)
 
Submission date Apr 23, 2019
Last update date Apr 02, 2021
Contact name Christoph J Binder
E-mail(s) cjbinderlab@gmail.com
Organization name Medical University of Vienna
Department Laboratory Medicine
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code A-1090
Country Austria
 
Platform ID GPL21290
Series (1)
GSE130225 mRNA expression in endothelial cells stimulated with isolated mitochondria
Relations
BioSample SAMN11484066
SRA SRX5726973

Supplementary file Size Download File type/resource
GSM3734143_S_67taras_S32426_genes_fpkm.tsv.gz 1.8 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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