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Status |
Public on Oct 01, 2022 |
Title |
BMDM_LPS_8h_1 |
Sample type |
SRA |
|
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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: 1
|
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.).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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|
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.
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Submission date |
Dec 19, 2020 |
Last update date |
Oct 01, 2022 |
Contact name |
Andrzej Dziembowski |
E-mail(s) |
adziembowski@iimcb.gov.pl
|
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 |
|
Relations |
BioSample |
SAMN17120510 |
SRA |
SRX9706769 |