|
| Status |
Public on Oct 01, 2022 |
| Title |
SA_TENT-5_3 |
| Sample type |
SRA |
| |
|
| Source name |
L4 worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: tent-5(tm3504) I (NBRP)
genotype: tent-5(tm3504) mutant
treatment: grown at 25℃ on TSA, infected by S. aureus NCTC8325 for 8h
tissue: whole worm
replicate: 3
|
| 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 |
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 |
GPL19757 |
| Series (1) |
| GSE163549 |
TENT5 cytoplasmic non-canonical poly(A) polymerases regulate the innate immune response in animals |
|
| Relations |
| BioSample |
SAMN17120514 |
| SRA |
SRX9706765 |
