 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 25, 2024 |
| Title |
Ku80 CUT&Tag 2 |
| Sample type |
SRA |
| |
|
| Source name |
tachyzoites
|
| Organism |
Toxoplasma gondii |
| Characteristics |
tissue: tachyzoites
genotype: RH
treatment: co-culture with DMSO vehicle for 24 h
|
| Treatment protocol |
Transgenic parasite strains cultured in Vero cells were treated with either 500 μM IAA or vehicle for 12h or 24 h.
|
| Growth protocol |
Transgenic strains were inoculated in 75 cm2 cell culture flasks and washed after 4 h to remove non-invasive parasites. Transgenic strains (1 x 107) were harvested after 20 h of incubation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For CUT&Tag Library construction, the library was performed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit for Illumina (Novoprotein, Suzhou, China) according to the manufacturer's instructions. Briefly, fresh tachyzoites were bound to activated concanavalin A beads (10 μL/sample) and incubated for 10 min at room temperature. The mixture was resuspended and incubated with primary antibody (1:50, mouse anti-HA) at 4°C overnight. After several washes, the parasites were incubated with secondary antibody (1:100, goat anti-mouse IgG) for 1 h at room temperature. The parasites were then resuspended with pAG-Transposome buffer and incubated for 1 h at room temperature on a rotator. Tagmentation was stopped by MgCl2 treatment and DNA extraction was performed using DNA extract beads (Novoprotein, Suzhou, China).
For CUT&Tag Library construction, Illumina sequencing libraries were generated by PCR amplification using specific adaptors according to the manufacturer’s recommendations (NovoNGS CUT&Tag 4.0 High-Sensitivity Kit for Illumina B box, Novoprotein, Suzhou, China).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CUT&Tag
|
| Data processing |
For CUT&Tag analysis, the paired-end reads were filtered and then aligned to the T. gondii reference genome using Bowtie2. The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Picard tools. The filtered reads were then employed to identify CUT&Tag peaks using MACS2. The overlapped peaks in the two biological replicates were identified by the Irreproducibility Discovery Rate (IDR).
Assembly: ToxoDB-57_TgondiiME49 genome
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&Tag
|
| |
|
| Submission date |
Aug 18, 2024 |
| Last update date |
Aug 25, 2024 |
| Contact name |
Dandan Hu |
| E-mail(s) |
[email protected]
|
| Organization name |
Guangxi University
|
| Street address |
Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.
|
| City |
Nanning |
| State/province |
China |
| ZIP/Postal code |
530004 |
| Country |
China |
| |
|
| Platform ID |
GPL26742 |
| Series (1) |
| GSE275112 |
Toxoplasma gondii transcription factor AP2XII-8 is a key regulator for the G1 phase progression and parasite division |
|
| Relations |
| BioSample |
SAMN43244949 |
| SRA |
SRX25751521 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8465746_1_Ctrl_2.bw |
6.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
