|
| Status |
Public on May 01, 2024 |
| Title |
ArR_30min_1, ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
cyst
|
| Organism |
Artemia parthenogenetic lineage |
| Characteristics |
tissue: cyst
genotype: WT
time: 30min after embryonic diapause termination (EDT)
|
| Treatment protocol |
At 30min 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 |
genomic DNA |
| Extraction protocol |
nuclei were extracted from each sample, and the nuclei pellet was re-suspended in the Tn5 transposase reaction mix.The transposition reaction was incubated at 37°C for 30 min. Equimolar adapter 1 and adapter 2 were added after transposition.
PCR was then performed to amplify the libraries. After the PCR amplification, libraries were purified with the AMPure beads and the quality of libraries was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2).
These reads were aligned to the Artemia genome using BWA, with standard parameters.
These reads were then filtered for high quality with MAPQ≥13 (i.e. p≤0.05), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt).
FastAC was used to evaluate the quality of the data.
Macs2 software was used for peak calling.
Assembly: ASM3288406v1
Supplementary files format and content: excel file contains the raw count, RPM values, gene ID and transcript ID for each peak
Supplementary files format and content: peak.xlsx
|
| |
|
| Submission date |
Feb 02, 2024 |
| 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) |
| GSE254934 |
ATAC-sequencing of Artemia cyst at 30min after embryonic diapause termination |
|
| Relations |
| BioSample |
SAMN39750075 |
| SRA |
SRX23510139 |
