|
| Status |
Public on Dec 18, 2020 |
| Title |
50_GACGAT: TNFα replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Bone marrow-derived macrophages (BMDM)
treament: TNFα
genotype: B6.129P2-Apoetm1Unc/J
|
| Treatment protocol |
Cells were pretreated with either TMP195 (5 µM) or TPCA-1 (500 nM) for 1 h prior to stimulation with TNF-α (50 ng/ml) for 24 h.
|
| Growth protocol |
Bone marrow-derived macrophages (BMDM) were generated as established by flushing the bone marrow from femurs and tibiae with ice-cold PBS, resuspending in PBS by repeated pipetting and filtering through a 40 µm cell strainer (BD Biosciences). After centrifugation of the cell suspension at 500 g for 10 min, the pellet was resuspended in culture medium (RPMI 1640 containing 10% FCS, 15% L929-cell-conditioned medium (LCM) and 100 µl/ml gentamycin) and plated on 15 cm untreated culture plates (Greiner). 15 % fresh LCM was added again on day 1 and 2 of culturing. For the stimulation experiments, differentiated macrophages were harvested by gentle scraping, transferred onto untreated 6-well or 12-well plates (Greiner) on Day 7 of culturing and left in LCM-free medium for 24 hours, allowing cells to adhere. Cells were then stimulated in FCS-free medium with either 50 ng/ml mouse recombinant TNF-α at different time intervals or left untreated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Sequenced reads were mapped to mm10 whole genome using STAR 2.6.1d with default parameters
STAR 2.6.1d was used to obtain read counts per gene based on ENSEMBL annotation Mus_musculus.GRCm38.95.gtf.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include STAR gene-based read counts for each sample
|
| |
|
| Submission date |
Nov 21, 2019 |
| Last update date |
Dec 18, 2020 |
| Contact name |
Tobias Straub |
| E-mail(s) |
tstraub@med.uni-muenchen.de
|
| Organization name |
LMU Munich
|
| Department |
Biomedical Center, Bioinformatics
|
| Street address |
Großhadener Str. 9
|
| City |
Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE140783 |
Histone deacetylase 9 promotes vascular inflammation by activating IKK |
|
| Relations |
| BioSample |
SAMN13343759 |
| SRA |
SRX7198250 |
