|
| Status |
Public on Feb 03, 2023 |
| Title |
N2 + vha-6 RNAi + elt-2 RNAi, rep 3 [exp2] |
| Sample type |
SRA |
| |
|
| Source name |
N2 + vha-6 RNAi + elt-2 RNAi, rep 3
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
genotype: WT
RNAi treatment: vha-6 RNAi 25percent + elt-2 RNAi 40percent + control RNAi 35percent
|
| Treatment protocol |
RNAi treatment was started from L1 and worms were collected after reaching L4/young adult stage in 2.5 days
|
| Growth protocol |
Synchronized worm eggs were obtained by alkaline hypochlorite treatment of gravid worms grown on E. coli OP50-seeded plates, which were transferred onto RNAi plates and cultured at for 2.5 days at 20°C to allow developing to L4/young adult phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On the day of the extraction, 1 ml of TriPure Isolation Reagent (Cat. 11667165001, Roche) was added to each tube. RNA was then extracted by using a column-based kit from Macherey-Nagel (Cat. 740955.250).
RNA libraries were prepared for sequencing using standard BGISeq500 protocols with polyA enrichment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
WH3
|
| Data processing |
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.fa --sjdbGTFfile Caenorhabditis_elegans.WBcel235.89.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)
|
| |
|
| Submission date |
Feb 03, 2022 |
| Last update date |
Feb 03, 2023 |
| Contact name |
Terytty Yang Li |
| E-mail(s) |
teryttyliyang@fudan.edu.cn
|
| Organization name |
EPFL
|
| Street address |
EPFL SV IBI-SV LISP AI 1145
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL25145 |
| Series (2) |
| GSE196022 |
LySR, a lysosomal surveillance response that extends healthspan [Exp2] |
| GSE196023 |
A lysosomal surveillance response that extends healthspan |
|
| Relations |
| BioSample |
SAMN25610550 |
| SRA |
SRX14028737 |
