|
| Status |
Public on Aug 16, 2023 |
| Title |
HBMEC_CM_SF_LDDD_D1 |
| Sample type |
RNA |
| |
|
| Source name |
HBMEC+CM M0SF+LDDD D1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: HBMEC
|
| Treatment protocol |
Serum-free or EV-conditioned media, collected from macrophages pre-conditioned were added to HBMECs for 6 h at 37°C in hypoxia.
|
| Growth protocol |
Cells were seeded in 24-well plates in full medium, followed by 24 h starvation in SF EC medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HBMEC samples were dissolved in 50 μl lysis solution provided by the AllPrep DNA/RNA Micro Kit for RNA isolation according to the manufacturer’s instructions. Total RNA quality was assessed by Agilent Technologies 2200 Tapestation and concentrations were measured by NanoDrop ND-1000 Spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
Fragmentation and labeling were performed with the GeneChip® WT Plus Labeling Kit according to the manufacturer’s instructions. 200 ng of total RNA was used to generate amplified sense strand cDNA targets using GeneChip® WT Plus Reagent Kit (ThermoFisher Scientific) followed by fragmentation and labelling of 5.5 ug sscDNA.
|
| |
|
| Hybridization protocol |
5.2 µg of fragmented and labelled sscDNA target was hybridized to Clariom™ D Human Arrays for 16 hours at 45°C under rotation in Affymetrix Gene Chip Hybridization Oven 645 (ThermoFisher Scientific). Washing and staining was carried out on Affymetrix GeneChip® Fluidics Station 450 (ThermoFisher Scientific), according to the manufacturer’s protocol.
|
| Scan protocol |
The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G (ThermoFisher Scientific).
|
| Description |
RNA extracted from HBMEC cells treated with serum-free conditioned media with LDDD, donor 1
|
| Data processing |
Processing of gene array was performed with method SST_RMA, with annotation done with Clariom_D_Human.r1.na36.hg38.a1.transcript.csv and statistics with limma's moderated t.
|
| |
|
| Submission date |
Jul 05, 2023 |
| Last update date |
Aug 16, 2023 |
| Contact name |
Mattias Belting |
| E-mail(s) |
mattias.belting@med.lu.se
|
| Organization name |
Lund University
|
| Department |
Clinical Sciences Lund
|
| Lab |
Tumor Microenvironment
|
| Street address |
Barngatan
|
| City |
Lund |
| State/province |
Skåne |
| ZIP/Postal code |
SE-221 85 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE236478 |
Clariom D gene array of HBMEC cells |
|
