|
| Status |
Public on Dec 21, 2022 |
| Title |
BMDM_Veh_LPS4h_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow-derived macrophage
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
|
| Treatment protocol |
For LPS treatment, 100 ng/ml of LPS (Sigma-Aldrich) was added to the medium.
|
| Growth protocol |
Bone marrow cells were flushed from femurs and tibias of male mice between 6 and 9 weeks of age, and were grown in RPMI (Nacalai Tesque) supplemented with 10% FBS (HyClone), 1% penicillin–streptomycin (Thermo Fisher), 1% L-glutamine (Thermo Fisher), and 40 ng/ml of recombinant mouse M-CSF (576406; BioLegend) for 7-8 days. The medium was changed every 3 days. Differentiated BMDMs were detached from plates using PBS supplemented with 2% EDTA and replated into 12-well tissue culture dishes at a density of 5 x 105 cells per well prior to cell stimulation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Poly-A mRNA was extracted from total RNA by using an NEBNext Poly(A) mRNA magnetic Isolation module (NEB), after which RNA-seq libraries were prepared using a NEBNext UltraII RNA Library Prep kit for Illumina (NEB) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Vehicle-treated, LPS-treated
|
| Data processing |
Reads were aligned to the mm9 mouse genome using STAR.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using Homer.
|
| |
|
| Submission date |
Mar 02, 2020 |
| Last update date |
Dec 21, 2022 |
| Contact name |
Ichiro Manabe |
| E-mail(s) |
manabe-tky@umin.ac.jp
|
| Organization name |
Chiba University
|
| Street address |
1-8-1 Inohana, Chuo
|
| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE146236 |
Analysis of effects of polyrotaxane on macrophages |
|
| Relations |
| BioSample |
SAMN14258961 |
| SRA |
SRX7827869 |
