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Sample GSM8662502

Query DataSets for GSM8662502

Status

Public on Dec 19, 2024

Title

ME49,HDAC3,biol rep 2

Sample type

SRA

Source name

toxoplasma

Organism

Toxoplasma gondii

Characteristics

cell type: toxoplasma
strain: ME49
chip antibody: rabbit anti-TgHDAC3(generated by immunizing rabbit with the synthetic peptide sequence 'CPYRIRRKDYANDFE' conjugated to KLH)

Growth protocol

ME49 and ME49ΔXII-5 were cultured in human foreskin fibroblasts (HFF), in Dulbecco’s Modified Eagle Medium (DMEM) (Sigma-Aldrich, USA), supplemented with 2% heat-inactivated fetal bovine serum (FBS) (Gibco, USA), 1% penicillin-streptomycin, and 5 mM L-glutamine.

Extracted molecule

genomic DNA

Extraction protocol

Intracellular parasites were released by needle passage and purified through filtration with 3 μm pore-size membranes. Approximately 5 x 10⁶ tachyzoites were collected and processed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China), following the manufacturer’s instructions.
The resulting DNA was amplified for library construction using the TD202 TruePrep Index Kit V2 for Illumina (Vazyme Biotech, China). The libraries were enriched, quantified, and sequenced on a NovaSeq 6000 sequencer (Illumina) using the PE150 model.

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina NovaSeq 6000

Description

Library name: ME49_IP_2

Data processing

raw sequencing data were initially filtered using cutadapt (version 2.5) to remove low-quality reads and trim adaptor-contaminated sequences
Clean reads were mapped to the T. gondii reference genome (TGME49) using Bowtie2 (version 2.3.4.1) with default parameters
Library quality was assessed by calculating insert sizes using samtools (version 1.12) and analyzing read distribution around transcription start sites (TSS) with deepTools (version 3.5.1)
Peak calling was performed using MACS2 (version 2.1.1, -p 0.01 --shift 75 –extsize 150 --nomodel -B –SPMR --keep-dup all --call-summits) and IgG controls for thresholdingBigwigs were generated using bigWigMerge and bedGraphToBigWig (version 4.11.1). Peaks were annotated using the ChIPseeker (version 1.32.1)
Bigwigs were generated using bigWigMerge and bedGraphToBigWig (version 4.11.1). Peaks were annotated using the ChIPseeker (version 1.32.1)
Assembly: T. gondii reference genome (TGME49)
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

Submission date

Dec 03, 2024

Last update date

Dec 19, 2024

Contact name

xue lilan

E-mail(s)

[email protected]

Phone

13763312131

Organization name

huazhong agriculture university