|
| Status |
Public on Jul 18, 2018 |
| Title |
mac53 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
L1 worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/genotype: skn-1(mac53)
developmental stage: L1
treatment: untreated
|
| Growth protocol |
Synchronized animals at the L1 larval stage were allowed to recover on OP50-seeded NGM agar plates with or without 5 mM NaI for 8 hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol (Invitrogen) and chloroform-isopropanol.
Libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw data was processed with Perl scripts to ensure the quality of data used in further analysis, clean data was obtained by removing reads Vontaining adapter.
Bowtie2 was used for building the genome index, and Clean Data was mapped to the WBcel235 alignments using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count.
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jul 17, 2018 |
| Last update date |
Jul 18, 2018 |
| Contact name |
Long Ma |
| Organization name |
Central South University
|
| Street address |
Xiangya Road No.110
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410078 |
| Country |
China |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE117222 |
WDR-23 and SKN-1 Nrf2 coordinate with the BLI-3 dual oxidase in response to iodide-triggered oxidative stress |
|
| Relations |
| BioSample |
SAMN09670242 |
| SRA |
SRX4398921 |
