|
| Status |
Public on Aug 13, 2020 |
| Title |
BMDMs Control 3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow derived macrophages
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Bone marrow derived macrophages
treatment: -
|
| Treatment protocol |
Macrophages were polarized to the M1 phenotype with 10 ng/ml interferon gamma (IFNγ, PeproTech, 214-14-2UG, lot 111249), to the M2 phenotype with 10 ng/ml interleukin 4 (IL-4, PeproTech, 315-05-20UG, lot 061398) or to erythrophagocytes like with 200 µM or 400 µM heme-albumin
|
| Growth protocol |
Bone marrow cells were obtained from the femurs and tibias of 8- to 10-week-old mice. The bone marrow murine stem cells were expanded and differentiated in RPMI medium supplemented with 10% FCS in the presence of recombinant mouse M-CSF (PeproTech 315-02-100UG, lot 0914245) at 10 ng/ml for 7 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Micro kit (Qiagen, Hombrechtikon, Switzerland) according to the manufacturer's protocol, including on-column DNase I treatment.
RNA samples using the Illumina TruSeq RNA stranded kit following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Heme-albumin preparation protocol: Hemin (heme-chloride) was obtained from Sigma (51280), and ZnPP was obtained from Frontiers (FSIZn625-9). The porphyrins were dissolved in 10 ml of NaOH (100 mM) at 37°C, followed by addition of 10 ml of 20% human serum albumin (CSL Behring AG). After 1 hour of incubation at 37°C, the pH of the solution was adjusted to pH 7.4 using ortho-phosphoric acid, and the final volume was brought to 25 ml with saline solution. The porphyrin-albumin solutions were sterile-filtered (0.22 µm) and used immediately.
|
| Data processing |
Reads were aligned to the reference genome using STAR (v2.7.0e).
The quality of alignment was evaluated using Samtools (v1.9).
Counts were obtained using the featureCounts function of the Rsubread package (v1.22.2).
Genome_build: Ensembl GRCm38.p5 Release 91
Supplementary_files_format_and_content: Output from feautrecount: table with raw count data of every genes (row) for each sample (column)
|
| |
|
| Submission date |
Feb 13, 2020 |
| Last update date |
Aug 13, 2020 |
| Contact name |
Marc Pfefferle |
| E-mail(s) |
marc.pfefferle@uzh.ch
|
| Organization name |
University hospital Zürich (USZ)
|
| Street address |
Wagistrasse 12
|
| City |
Schlieren |
| State/province |
Schweiz |
| ZIP/Postal code |
8952 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE145243 |
Erythrophagocytosis drives anti-inflammatory programming of liver macrophages (Bulk RNA seq BMDMs) |
| GSE145244 |
Erythrophagocytosis drives anti-inflammatory programming of liver macrophages |
|
| Relations |
| BioSample |
SAMN14094210 |
| SRA |
SRX7717691 |
