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| Status |
Public on Jan 30, 2023 |
| Title |
IWS1 KO parasite_3 |
| Sample type |
SRA |
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| Source name |
tachyzoites
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| Organism |
Toxoplasma gondii |
| Characteristics |
cell type: tachyzoites
genotype: IWS1 knock out
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells with a miRNeasy Mini kit (Qiagen) following the manufacturer’s instruction.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the Toxoplasma gondii (GCA_000149715.2_TGGT1) reference genome using hisat2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
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| Submission date |
May 26, 2022 |
| Last update date |
Jun 06, 2024 |
| Contact name |
Daisuke Motooka |
| E-mail(s) |
[email protected]
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| Organization name |
NGS core facility, Research Institute for Microbial Diseases, Osaka University
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| Street address |
3-1, Yamadaoka
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| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
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| Platform ID |
GPL26742 |
| Series (1) |
| GSE204926 |
Toxoplasma IWS1 determines fitness in interferon-γ-activated host cells and mice by regulating ROP18 mRNA expression |
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| Relations |
| BioSample |
SAMN28685944 |
| SRA |
SRX15474035 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6202449_IWS1KO-3_FPKM.txt.gz |
54.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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