|
| Status |
Public on Oct 01, 2022 |
| Title |
HB_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 plates seeded with E. coli HB101
tissue: whole worm
replicate: 2
|
| Treatment protocol |
Synchronized wild-type and mutant worms were grown at 25°C on NGM plates seeded with E. coli HB101 until they reached the L4 stage. Worms were washed 3x with 50 mM NaCl and resuspended in 1 ml of TRI Reagent (Sigma-Aldrich)
|
| 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 |
SAMN17120524 |
| SRA |
SRX9706755 |
