Background

Toxoplasma gondii is a common protozoan parasite that can infect up to one-third of the world's population. At present, human cells have little knowledge of the innate immune induction mechanism of this obligate intracellular parasite. And the principle of infection has not yet been fully studied.

Protocol

PBMCs were isolated from the heparinized peripheral blood of 20 healthy volunteers, cultured in vitro and infected with Pru and RH88 factors, and then sequenced and analyzed their expression profiles.

Result

RNA sequencing analysis of changes in gene expression levels of human peripheral blood after infection with Toxoplasma gondii for 12 hours reveals that human monocytes recognize the presence of Toxoplasma gondii by recognizing the S100A11 protein. S100A11 induces a strong chemokine response by activating the receptor RAGE of Toxoplasma gondii.

S100A11 induces the expression of chemokine CCL2 to regulate the recruitment of monocytes in vivo.

v2.0: The process is automated, the code is uploaded to the CRS platform, the software is uploaded to the SRS platform, and the reference genome is uploaded to the DRS platform, making it possible to combine with other processes.

v1.2: Add parameter modification function, support custom parameters.

v1.1: Selection and replacement of related software.

v1.0: Process construction, complete the basic process of data quality control, comparison, and differential gene calculation.

Instruction for Upload File

1. A compressed file containing the data to be analyzed

(1). If the data is not stored on this platform, upload the data from Website to use the analysis protocol. Please compress all data into a single file. (supported compression formats: rar, zip, gz, tar.gz.)

(2). If the data to be analyzed has been stored on this platform (DRS or Local), please upload any content compressed file that conforms to the format.

2. Data basic information and project parameter json file.

Support to modify the parameters as follows:

(1). "dataId"

If the data has been stored in this platform (DRS), DRS id is needed.

(2). "dataFrom": "DRS", "Local", "Web"

Source of the analyzed data.

(3). "SampleGroup": "Case", "Control"

Sample classification

(4). "SampleName"

Sample name

(5). "OmicLocation": "RNA", "DNA"

Sequencing category

(6). "Pipeline"

Which pipeline to used. (fixed in this project)

(7). "SeqRegion": "RRBS", "WGBS", "Target"

The sequencing area of this sample is RRBS (MspI enzyme), WGBS, or Targeted bisulfite sequencing.

(8). "SeqPlatform": "Illumina", "SOLiD", "Roche454"

Sequencing platform

(9). "SeqReadType": "Single_end", "Paired_end"

The sample is single-end sequencing or paired-end sequencing.

(10). "FileType": "sra", "fq", "fq.gz", "fastq", "fastq.gz"

The sample file format.

(11). "fileName"

The name of the data to be analyzed (including file type).

If the data contains only a single file (such as single-end sequencing data or .sra suffix file), just fill in the file name; if the data contains multiple files (such as paired-end sequencing data file_{1,2}.fq. gz), you need to fill in "fillName" and "FilenameR2" at the same time.

(12). "FilenameR2"

If the data contains multiple files (for example: paired-end sequencing data file_{1,2}.fq.gz), you need to fill in "fillName" and "FilenameR2" at the same time.

(13). "AlignmentSoftware"

The comparison software used in the process. Default is Hisat2.

(14). "Race"

Sequencing samples. The default is the whole population.

(15). "Do_QC": "yes", "no"

Whether to perform data quality control. It is recommended to choose "yes" unless the data has been trimmed.