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Sample GSM4981582 Query DataSets for GSM4981582
Status Public on Oct 01, 2022
Title SA_WT_2
Sample type SRA
 
Source name L4 worms
Organism Caenorhabditis elegans
Characteristics strain: N2 Bristol (CGC)
genotype: wild type
treatment: grown at 25℃ on TSA, infected by S. aureus NCTC8325 for 8h
tissue: whole worm
replicate: 2
Treatment protocol Synchronized wild-type and mutant worms were grown on NGM plates seeded with E. coli HB101 at 25°C until they reached the L4 stage. The infection plates were prepared as described (Visvikis et al., 2014). In brief, TSA plates with 10 μg/ml Nalidixic acid were prepared one week before the experiment and stored at 4°C in the dark. S. aureus was grown in TSB + Nal overnight at 37°C. 500 μl of the overnight S. aureus culture was uniformly spread onto the entire surface of 100 mm TSA + Nal plates and incubated at 37°C for 6 h. L4 worms were washed three times with sterile 50 mM NaCl and seeded onto infection TSA plates that were previously warmed to RT. After 8 h of infection at 25°C, animals were washed off the plates and resuspended in 1ml of 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
E-mail(s) pkrawczyk@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 GPL19757
Series (1)
GSE163549 TENT5 cytoplasmic non-canonical poly(A) polymerases regulate the innate immune response in animals
Relations
BioSample SAMN17120518
SRA SRX9706761

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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