|
| Status |
Public on May 01, 2024 |
| Title |
RNA ArR_5h_3 |
| Sample type |
SRA |
| |
|
| Source name |
cyst
|
| Organism |
Artemia parthenogenetic lineage |
| Characteristics |
tissue: cyst
cell line: Artemia parthenogenetica
cell type: cyst
genotype: WT
treatment: the dry cysts were thoroughly rehydrated in ice-cold 30‰ artificial seawater and reactivated in 30‰ artificial seawater at 28 C under continuous illumination.
|
| Treatment protocol |
For diapause stage and 5 h after diapause breaking, the dry cysts were thoroughly rehydrated in ice-cold 30‰ artificial seawater and reactivated in 30‰ artificial seawater at 28 °C under continuous illumination. Each sample was quickly collected and put in liquid nitrogen immediately and then preserved in a −80 °C refrigerator.
|
| Growth protocol |
Artemia parthenogenetica cysts (provided by Asian Regional Artemia Reference Center, ARARC) were collected in Ebinur Lake and reactivated after dehydration and refrigeration treatment to break diapause.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA from Artemia cysts was isolated using TRIzol reagent and treated with RNase-free DNase I to remove any contaminating genomic DNA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina). After cluster generation, the library preparations were sequenced on an Illumina novaseq platform and 150 bp paired-end reads were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The original image data were transferred into sequencing data by base calling and generate raw reads.
Clean data including clean reads were obtained by removing the raw reads which contains an adapter, poly-N or with low quality.
Subsequently, Q20, Q30 and GC contents of the clean data were calculated for the quality control.All the downstream analysis was based on the high quality clean data.
Artemia genome from NCBI database was used as the reference genome for genome mapping. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. The FPKM of each gene was calculated based on the length and reads count mapped to the gene. FPKM is the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Assembly: Artemia genome from NCBI database
Supplementary files format and content: excel file contains the raw count and fpkm values for each sample
|
| |
|
| Submission date |
Dec 05, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Tong Hao |
| E-mail(s) |
skyht@tjnu.edu.cn
|
| Organization name |
College of Life Sciences, Tianjin Normal University
|
| Department |
College of Life Sciences
|
| Street address |
No.393
|
| City |
Tianjin |
| State/province |
China |
| ZIP/Postal code |
300387 |
| Country |
China |
| |
|
| Platform ID |
GPL33946 |
| Series (1) |
| GSE249417 |
Transcriptome profiling of Artemia cyst in in diapause stage and 5 hours after embryonic diapause termination |
|
| Relations |
| BioSample |
SAMN38680102 |
| SRA |
SRX22788099 |
