Dataset overview

This dataset contains transcriptome sequencing results from human microvascular endothelial cells (HMEC-1). Cells were divided into two groups:

1. Control group: treated with PBS (n = 3 biological replicates)
2. Experimental group: treated with anti-TP0136 antibody (n = 3 biological replicates)

The dataset captures gene-level raw read counts, normalized TPM values, fold-change statistics, statistical significance values, and functional annotations to investigate transcriptional changes induced by anti-TP0136 antibody.

File information:

Filename: sample_data.csv

File format: comma-separated values (CSV)

Columns: gene identifiers, expression measurements, differential expression statistics, and functional annotations

Variables:

• id: Ensembl gene ID.
• Control-1_count: Raw read count for PBS-treated control biological replicate 1.
• Control-2_count: Raw read count for PBS-treated control biological replicate 2.
• Control-3_count: Raw read count for PBS-treated control biological replicate 3.
• Antibody-1_count: Raw read count for anti-TP0136 antibody-treated biological replicate 1.
• Antibody-2_count: Raw read count for anti-TP0136 antibody-treated biological replicate 2.
• Antibody-3_count: Raw read count for anti-TP0136 antibody-treated biological replicate 3.
• Control-1_tpm: Normalized expression value, in transcripts per million (TPM), for PBS-treated control biological replicate 1.
• Control-2_tpm: Normalized expression value, in transcripts per million (TPM), for PBS-treated control biological replicate 2.
• Control-3_tpm: Normalized expression value, in transcripts per million (TPM), for PBS-treated control biological replicate 3.
• Antibody-1_tpm: Normalized expression value, in transcripts per million (TPM), for anti-TP0136 antibody-treated biological replicate 1.
• Antibody-2_tpm: Normalized expression value, in transcripts per million (TPM), for anti-TP0136 antibody-treated biological replicate 2.
• Antibody-3_tpm: Normalized expression value, in transcripts per million (TPM), for anti-TP0136 antibody-treated biological replicate 3.
• C_mean: Mean TPM value across the three PBS-treated control replicates.
• A_mean: Mean TPM value across the three anti-TP0136 antibody-treated replicates.
• FC(A/C): Fold change calculated as A_mean divided by C_mean. Values greater than 1 indicate higher expression in the anti-TP0136 antibody-treated group compared with the PBS-treated control group.
• log2(fc): Log2-transformed fold change based on FC(A/C). Positive values indicate higher expression in the anti-TP0136 antibody-treated group, while negative values indicate lower expression.
• PValue: Statistical P value from differential expression analysis comparing anti-TP0136 antibody-treated samples with PBS-treated control samples.
• FDR: False discovery rate-adjusted P value for multiple testing correction.
• Symbol: HGNC official gene symbol.
• Description: Gene description from HGNC.
• KEGG_A_class: KEGG top-level pathway classification.
• KEGG_B_class: KEGG second-level pathway classification.
• Pathway: KEGG pathway name and pathway identifier associated with the gene.
• K_ID: KEGG Orthology identifier associated with the gene.
• GO Component: Gene Ontology cellular component annotation.
• GO Function: Gene Ontology molecular function annotation.
• GO Process: Gene Ontology biological process annotation.
• TF_family: Assigned transcription factor family, if applicable. Entries marked as "--" indicate that no transcription factor family assignment was available.

Abbreviations:

• PBS: phosphate-buffered saline.
• HMEC-1: human microvascular endothelial cell line.
• TPM: transcripts per million.
• FC: fold change.
• FDR: false discovery rate.
• HGNC: HUGO Gene Nomenclature Committee.
• KEGG: Kyoto Encyclopedia of Genes and Genomes.
• GO: Gene Ontology.
• TF: transcription factor.

Experimental methods

• Cell line: HMEC-1 (human microvascular endothelial cells)
• Treatment: PBS vs anti-TP0136 antibody
• Replicates: 3 biological replicates per group
• Sequencing: RNA-seq using an Illumina platform
• Processing: Reads were aligned to the human reference genome, gene-level raw counts were generated, and expression values were normalized to TPM. Differential expression statistics, including fold change, log2 fold change, P value, and FDR-adjusted P value, were calculated to compare the anti-TP0136 antibody-treated group with the PBS-treated control group. Functional annotations, including KEGG, GO, and transcription factor family information, were added for interpretation.

Potential reuse

This dataset can be reused for:

• Differential gene expression analysis between PBS-treated and anti-TP0136 antibody-treated HMEC-1 cells.
• Validation of angiogenesis-related pathways, including VEGF-A signaling.
• Meta-analysis of endothelial cell transcriptional responses.
• Integration with other syphilis-related, angiogenesis-related, or endothelial cell transcriptome datasets.

Legal and ethical statement

This dataset is derived from HMEC-1 immortalized human endothelial cells, not from human subjects.

No personal or sensitive information is included.

Data are released under the CC0 license and may be freely reused.