|
| Status |
Public on Apr 04, 2024 |
| Title |
Caenorhabditis elegans,20℃,middle adult,rep1 |
| Sample type |
SRA |
| |
|
| Source name |
middle stage ADF
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole body
tissue: middle stage ADF
age: adult
cell type: hermaphrodite
genotype: WT
treatment: M9
|
| Treatment protocol |
For the corresponding stages of worms, administer alternate day fasting (ADF) for a period of seven days, followed by the collection of a large number of nematodes for RNA extraction.
|
| Growth protocol |
Harvest worms and collect eggs simultaneously. The eggs were cultured in M9 and incubated at 20℃ until L1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1ug of total RNA for the construction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for base-calling
Sequenced reads were trimmed for adaptor sequence. and masked for low-complexity or low-quality sequence. then mapped to WBcel235 whole genome using bowtie v0.12.2 with parameters
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level was calculated through a protocol from Chepelev et al., Nucleic Acids Research,2009.
Assembly: C. elegans genome version WBcel235 was used as the reference.
Supplementary files format and content: The txt format file contains the FPKM value of expression gene
|
| |
|
| Submission date |
Mar 27, 2024 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Shanqing Zheng |
| E-mail(s) |
zhengshanqing@henu.edu.cn
|
| Phone |
+8637122892869
|
| Organization name |
Henan university
|
| Street address |
1 Jinming Avenue North, Longting District, School of Basic Medical Sciences, Henan University
|
| City |
Kaifeng |
| ZIP/Postal code |
475004 |
| Country |
China |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE262666 |
RNA-seq analysis of the young stage ADF, middle stage ADF, and the control worms |
|
| Relations |
| BioSample |
SAMN40634843 |
| SRA |
SRX24083319 |
