|
| Status |
Public on Sep 23, 2022 |
| Title |
N2 + cco-1 RNAi + vha-1 RNAi_rep2 [I2] |
| Sample type |
SRA |
| |
|
| Source name |
N2 + cco-1 RNAi + vha-1 RNAi_rep2
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
RNAi clone: E. coli HT115, cco-1 RNAi, vha-1 RNAi
genotype: Wild-type
stage at harvesting: L4/young adult
|
| Treatment protocol |
RNAi treatment was started from the egg phase and treated until worms reached L4/young adult phase and then collected in 1.5 mL tubes
|
| Growth protocol |
Worms were synchronized by bleaching. Synchronized worm eggs were plated in NGM plates under the described conditions and raised at 20 ̊C. Worms were harvested after 2 days (at L4/young adult stage) and washed with M9 buffer for three times to remove the bacteria, then snap frozen in liquid nitrogen.
|
| 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. The samples were then frozen and thawed quickly 8 times in liquid nitrogen to rupture cell membranes. 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 protocol with polyA enrichment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| 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.
Sequenced reads were mapped to the WBcel235 assembly of the worm genome using ensembl release 89 gene annotation with STAR aligner version 2.6.0a
Reads were counted using htseq-count version 0.10.0 using these flags: -f bam -r pos -s no -m union -t exon -i gene_id
Genome_build: Caenorhabditis_elegans.WBcel235.89
Supplementary_files_format_and_content: xlsx file with counts per gene per sample
|
| |
|
| Submission date |
Jul 06, 2021 |
| Last update date |
Sep 25, 2022 |
| 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 (1) |
| GSE179517 |
V-ATPase/TORC1-mediated ATFS-1 translation directs mitochondrial UPR activation in C. elegans |
|
| Relations |
| BioSample |
SAMN20079470 |
| SRA |
SRX11359587 |
