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Sample GSM4981592 Query DataSets for GSM4981592
Status Public on Oct 01, 2022
Title BMDM_LPS_8h_3
Sample type SRA
Source name bone marrow-derived macrophages
Organism Mus musculus
Characteristics strain: C57BL/6J;CBA
genotype: wild type
treatment: LPS-activated for 8h
cell type: bone marrow-derived macrophages
replicate: 3
Treatment protocol The primary BMDM cell cultures were established from the bone marrow monocytes from wild-type mice and cultured in IMDM medium (Thermo Fisher Scientific) supplemented with macrophage colony-stimulating factor (M-CSF, Preprotech) at 37°C in 5% CO2 as described previously (Graczyk et al., 2015). For BMDM stimulation with lipopolysaccharide (LPS), cells were treated with 100 ng/ml LPS (Santa Cruz Biotechnology) for 8 h. Cells were scratched from the plates, pelleted by centrifugation for 3 min at 350 x g, and resuspended in TRI Reagent.
Extracted molecule total RNA
Extraction protocol Total RNA from C. elegans and BMDM cells was isolated with TRI Reagent (Sigma-Aldrich) according to the manufacturer’s instructions. Before RNA-seq library preparation, total RNA samples were treated with TURBO DNase (Thermo Fisher Scientific) to remove DNA contamination. RNA was then purified by phenol/chloroform extraction and ethanol precipitation.
Ribosomal RNA was removed from samples using a Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat, Epicentre). Strand-specific libraries were prepared using a dUTP protocol (KAPA Stranded RNA-Seq Library Preparation Kit), according to the manufacturer. Library quality was assessed using chip electrophoresis performed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Illumina bcl2fastq 2.20 software used for basecalling.
Sequence reads from C. elegans experiments were mapped to the WBCel235 genome build (ENSEMBL, release 94) using STAR v. 2.6.1b
Sequence reads from M. musculus were mapped to the GRCm38 mouse genome build (ENSEMBL, release 94) using STAR v. 2.7.6a
Counts for each transcript in C. elegans experiments were collected using featureCounts from Subread package (v. 1.6.3), with options options -Q 10 -p -B -C -s 2 -g gene_id -t exon and respective annotation gtf file (WBCel235; ENSEMBL; release 94)
Counts for each transcript in M. musculus experiments were collected using featureCounts from Subread package (v. 2.0.1), with options options -Q 10 -p -B -C -s 2 -g gene_id -t exon and respective annotation gtf file (Gencode, vM25)
Differential expression analysis was performed using DESeq2, with default settings
Genome_build: GRCm38
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalized counts for each sample.
Submission date Dec 19, 2020
Last update date Oct 01, 2022
Contact name Paweł S Krawczyk
Organization name International Institute Of Molecular And Cell Biology In Warsaw
Lab Laboratory of RNA Biology
Street address 4 Ks. Trojdena Street
City Warsaw
ZIP/Postal code 02-109
Country Poland
Platform ID GPL19057
Series (1)
GSE163549 TENT5 cytoplasmic non-canonical poly(A) polymerases regulate the innate immune response in animals
BioSample SAMN17120508
SRA SRX9706771

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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