|
| Status |
Public on Nov 17, 2016 |
| Title |
THP-1 cells exposed at Arnica m. centesimal dilution 9c |
| Sample type |
SRA |
| |
|
| Source name |
THP-1 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
treatment: exposed at Arnica m. centesimal dilution 9c
|
| Treatment protocol |
Macrophages were exposed for 24 h to Arnica m. centesimal dilutions (2c, 3c, 5c, 9c, 15c) or control solvent (1 ml cell culture + 110 μl test solutions).
|
| Growth protocol |
The THP-1 cell line was cultured in RPMI 1640 medium, supplemented with FBS 10% and 2mM final concentration of Ultraglutamine (Lonza), at 37°C in 5% CO2 in a humidified incubator as described (Olioso et al., submitted). Briefly, in a typical experiment, on day one the cells were seeded at a density of 2.5x105 cells/mL in 24-well plates in 1 ml medium with 2mM Ultraglutamine and 2% FBS. On day 2 all the cell cultures were supplemented with 20 ng/mL of PMA and on day 3 the cultures were treated with IL-4 at a concentration of 50 ng/mL for 24h. On day 4 the plates were washed twice with culture medium and the cultures were again supplemented with 50 ng/mL IL-4 and incubated for 24h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy mini Kit (Qiagen).
RNA aliquots (2.5μg) were used to isolate poly(A) mRNA for the preparation of a directional Illumina RNA-Seq library using the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
A9C
|
| Data processing |
Alignment to human reference genome with TopHat 2.0.14 with default parameters
Quantification of reads mapping to Ensembl GRCh38.80 gene models using Rsamtools, GenomicFeatures and GenomicAlignments R packages with the "Union" overlap mode.
Transformation of raw read counts to Reads Per Kilobase of gene model per Millions of mapped reads (RPKM)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text containing RPKM expression values
|
| |
|
| Submission date |
Jan 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alberto Ferrarini |
| E-mail(s) |
alberto.ferrarini@univr.it
|
| Phone |
+39-045-802-7058
|
| Organization name |
University of Verona
|
| Department |
Scientific and Technological Department
|
| Lab |
Plant Functional Genomics Centre
|
| Street address |
Strada le Grazie, 15
|
| City |
Verona |
| State/province |
Veneto |
| ZIP/Postal code |
37134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE77381 |
Arnica montana stimulates extracellular matrix gene expression in human macrophages differentiated to wound-healing phenotype. Tested on 5 concentrations. |
|
| Relations |
| BioSample |
SAMN04448155 |
| SRA |
SRX1553079 |
