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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 13, 2020 |
| Title |
Macrophages SPTA CTRL 2 |
| Sample type |
SRA |
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| Source name |
Non-parenchymal liver cells enriched for F4/80 positive macrophages
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
cell type: Non-parenchymal liver cells enriched for F4/80 positive macrophages
genotype: Spta sph/sph
treatment: Saline i.p.
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| Treatment protocol |
Saline i.p. or agonistic anti-CD40 antibody i.p. 20 mg/kg 30h injection
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| Growth protocol |
8-10 week old male mice
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| Extracted molecule |
total RNA |
| Extraction protocol |
The abdominal cavity of a living, deeply anesthetized mouse was opened, and the portal vein was catheterized for in situ liver perfusion and digestion with 50 ml of 0.06 U/ml collagenase B buffered solution (Roche, 11088815001). Once digested, livers were dissected out and the mouse was sacrificed. The digested livers were then mechanically disaggregated in a petri dish on ice and filtered through a 100 μm pore cell strainer. The cell suspensions were centrifuged twice at 60 x g for 2 min at 4°C, and the pellets were discarded. The supernatants were then centrifuged at 300 x g for 5 min at 4°C to obtain a pellet of nonparenchymal liver cells containing liver macrophages. To select for F4/80+ macrophages from liver cell suspensions, Dynabeads Sheep anti-Rat IgG (Invitrogen, 11035), in combination with purified rat anti-mouse F4/80 antibody (BD Pharmingen, 0.5 mg/ml, 565409) ), and a DynaMag™-2 Magnet (Thermo Fisher Scientific, 12321D) were used according to the manufacturer's protocol (Invitrogen)
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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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)
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| Submission date |
Feb 13, 2020 |
| Last update date |
Aug 13, 2020 |
| Contact name |
Marc Pfefferle |
| E-mail(s) |
marc.pfefferle@uzh.ch
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| Organization name |
University hospital Zürich (USZ)
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| Street address |
Wagistrasse 12
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| City |
Schlieren |
| State/province |
Schweiz |
| ZIP/Postal code |
8952 |
| Country |
Switzerland |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE145242 |
Erythrophagocytosis drives anti-inflammatory programming of liver macrophages (Bulk RNA seq SPTA CD40 mac) |
| GSE145244 |
Erythrophagocytosis drives anti-inflammatory programming of liver macrophages |
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| Relations |
| BioSample |
SAMN14094189 |
| SRA |
SRX7717681 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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