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| Status |
Public on Dec 10, 2023 |
| Title |
Cut-Tag-AP2V-2-IAA-1 |
| Sample type |
SRA |
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| Source name |
T. gondii
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| Organism |
Toxoplasma gondii |
| Characteristics |
cell type: T. gondii
genotype: RH
treatment: IAA treated
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNAs from T. gondii tachyzoites were then extracted using the M5 Total RNA Extraction Reagent (Mei5 Biotechnology Co., Ltd, Beijing) according to the manufacturer’s protocol. Cut&tag DNA extraction was performed using DNA extract beads (Vazyme, Jiangsu, China)
RNA-SEQ libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations. Cut&tag libraries were generated by PCR amplification with specific adaptors according to the manufacturer’s recommendations (TruePrep Index Kit V4 for Illumina, Vazyme, Nanjing, China)
RNA-SEQ; CUT&TAG
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The RNA-SEQ Paired-end clean reads were aligned to the reference genome using Hisat2. Read counts for each gene were calculated using the sorted bam files using StringTie. Differentially expressed genes (DEGs) between treated and untreated parasites were calculated by edgeR.
For cut&tag peak calling, the paired-end reads were filtered and then aligned to the T. gondii reference genome using Bowtie2 (v.2.1.0). The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Sambamba. The filtered reads were then employed to identify Cut-Tag peaks using MACS2. The overlapped peaks in two biological replicates were identified by the Irreproducibility Discovery Rate (IDR). The final peaks were annotated against the latest T. gondii data in ToxoDB.
Assembly: reference genome of Toxoplasma Type II ME49 strain (ToxoDB-57)
Supplementary files format and content: .count files are the raw read count files of RNA-SEQ data. .bw files are the bigwig files for the cut&tag peaks.
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| Submission date |
Dec 07, 2023 |
| Last update date |
Dec 10, 2023 |
| Contact name |
Dandan Hu |
| E-mail(s) |
[email protected]
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| Organization name |
Guangxi University
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| Street address |
Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.
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| City |
Nanning |
| State/province |
China |
| ZIP/Postal code |
530004 |
| Country |
China |
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| Platform ID |
GPL26742 |
| Series (1) |
| GSE249604 |
AP2XII-1 and AP2XI-2 Suppress Schizogony Gene Expression in Toxoplasma gondii |
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| Relations |
| SRA |
SRX21482984 |
| BioSample |
SAMN37150112 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7951519_AP5_1.bw |
30.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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