|
| Status |
Public on Jun 04, 2019 |
| Title |
LPS-stimulated Bone Marrow-Derived Macrophages (4h) [mm_BMDM_LPS4h_RS206] |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Wild type
cell type: Bone Marrow-Derived Macrophages
stimulation: 4h, 10ng/ml, LPS
|
| Treatment protocol |
VSMC, BMDM and DC were left unstimulated or treated with single stimulus as follows: 1000U/ml of IFN alpha or 10ng/ml of IFN gamma for 8 hours; 10ng/ml (BMDM and DC)/1μg/ml (VSMC) of LPS for 4 hours. To further study the effect of IFNs pretreatment on LPS signaling, the cells were first treated with IFN alpha/IFN gamma for 8 hours followed by LPS stimulation for another 4 hours, as abovementioned.
|
| Growth protocol |
VSMC were cultured in DMEM complete medium supplemented with 10% FBS, 1:100 L-glutamine and 1:100 antibiotic/antimycotic solution. On the day before treatment, complete medium was exchanged onto 2% FBS containing starving medium. Differentiated BMDM and DC were immediately placed in serum free medium or 2% FBS containing RMPI1640 supplemented with 1:100 antibiotic/antimycotic solution and 50μM β-ME, respectively, for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from primary VSMC, BMDM and DC was isolated with GeneMATRIX Universal RNA Purification Kit (EURx) according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mm_BMDM_LPS4h_RS206
|
| Data processing |
Alignment with TopHat v2.0.7 using default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: N/A
|
| |
|
| Submission date |
Oct 03, 2018 |
| Last update date |
Jun 04, 2019 |
| Contact name |
Anna Piaszyk-Borychowska |
| E-mail(s) |
[email protected]
|
| Organization name |
Adam Mickiewicz University
|
| Department |
Department of Human Molecular Genetics
|
| Street address |
ul. Umultowska 89
|
| City |
Poznań |
| ZIP/Postal code |
61-614 |
| Country |
Poland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE120807 |
Genome-wide collaboration of canonical and non-canonical STAT1 complexes with NF-κB to control signal integration between Interferons and TLR4 in vascular and immune cells [RNA-seq] |
| GSE120808 |
Genome-wide collaboration of canonical and non-canonical STAT1 complexes with NF-κB to control signal integration between Interferons and TLR4 in vascular and immune cells |
|
| Relations |
| BioSample |
SAMN10174259 |
| SRA |
SRX4796097 |
