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Sample GSM3993142 Query DataSets for GSM3993142
Status Public on Jul 16, 2021
Title EXO_13
Sample type SRA
 
Source name Exosome-depleted conditioned medium for 24h
Organism Homo sapiens
Characteristics strain: human lympahtic endothelial cells HMVECs (Lonza)
treatment: DMEM+secreted factors from SK-MEL-147 cells growing for 72h (conditioned medium). Medium was depleted of exosomes by ultracentrifugation
Treatment protocol 5 μg/mL of freshly purified exosomes were added in a volumen of 20 μL to the cells. For conditioned medium treatment 500 μL of exosome-depleted supernantants of SK-MEL-147 cells growing in DMEM were added to 500μL of EGM-2MV in each well
Growth protocol Cell were growing on gelatin-coated 6-well plates for 24h in 1 mL of EGM-2MV medium before treatments were added. Fresh medium was added when treatments started
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using Trizol Reagent (Invitrogen). After the recovery of the aqueous phase using chlorophorm, a DNAse treatment was performed using the Mini RNeasy kit (Qiagen) following manufacturer instructions.
cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit, and sequenced on a Illumina HiSeq1500 sequencer.
Unstranded RNA-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description Isolation of poly A+ RNA from total RNA
Unstranded RNA-seq
Data processing RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the human GRCh37/hg19 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM values calculated with Cuffnorm
 
Submission date Jul 31, 2019
Last update date Jul 16, 2021
Contact name Osvaldo Graña
Organization name CNIO
Department Structural Biology
Lab Bioinformatics Unit
Street address C/ Melchor Fernández Almagro, 3
City Madrid
State/province Comunidad de Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL18460
Series (1)
GSE135187 RNA profiling of human lymphatic endothelial cells exposed to melanoma exosomes
Relations
BioSample SAMN12405944
SRA SRX6624136

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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