|
Status |
Public on Jul 16, 2021 |
Title |
EXO_3 |
Sample type |
SRA |
|
|
Source name |
Control
|
Organism |
Homo sapiens |
Characteristics |
strain: human lympahtic endothelial cells HMVECs (Lonza) treatment: only volumen of PBS corresponding to volumen of exosomes
|
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 |
SAMN12405936 |
SRA |
SRX6624141 |