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Sample GSM7886869

Query DataSets for GSM7886869

Status

Public on Feb 09, 2024

Title

LysM-Cre IL10R fl/fl #2

Sample type

SRA

Source name

liver

Organism

Mus musculus

Characteristics

tissue: liver
cell type: sorted myeloid cells
genotype: LysM-Cre IL10R fl/fl

Extracted molecule

polyA RNA

Extraction protocol

Murine livers were harvested after PBS perfusion and gallbladder removal, cut into small pieces and digested in HBSS (with Ca2+ and Mg2+) containing 10 U/ml DNase and 1 mg/ml Collagenase, in a shaking incubator at 37°C for 25 minutes. After digestion, the livers were smashed and washed using PBS (1% FBS) through a cell strainer to a single cell resolution, and the pellet was collected after centrifugation at 400 g for 8 minutes. Immune cells were then enriched from the pellet by Percoll gradient centrifugation (GE Healthcare, Chicago, IL). Immune cells were then FACS sorted, with myeloid cells being gated as CD45+ CD3- CD11c- CD11b+. RNA was isolated from sorted cells using Trizol (Invitrogen).
libraries were constructed using polyA enrichment

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Sequencing quality was assessed with FastQC v. 0.11.5, followed by trimming of low quality bases with Trimmomatic v. 0.33 and alignment to the Mus musculus genome draft GRCm38.84 using STAR v. 2.5.0.
Assembly: GRCm38.84
Supplementary files format and content: Raw counts summarized per gene for each sample after alignment with STAR

Submission date

Nov 08, 2023

Last update date

Feb 09, 2024

Contact name

Babett Steglich

Organization name

Universitätsklinikum Hamburg-Eppendorf

Street address

Martinistrasse 52

City

Hamburg