|
| Status |
Public on Jul 16, 2021 |
| Title |
EXO_14 |
| 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 |
SAMN12405943 |
| SRA |
SRX6624137 |
