Human conjunctival transcriptome in Acanthamoeba keratitis: An exploratory study

The host conjunctival transcriptome of 9 patients with Acanthamoeba keratitis (AK) is compared to the conjunctival transcriptome of 13 patients with keratitis and no identified pathogen. Pathway enrichment analysis identified thirty-six transcripts as most differentially expressed between patients with AK compared to patients with presumed sterile keratitis., The host conjunctival transcriptome of 9 patients with Acanthamoeba keratitis (AK) is compared to the conjunctival transcriptome of 13 patients with keratitis and no identified pathogen. For the differential host gene expression analysis, sequencing reads were quality filtered and aligned to the GRCh38 human genome assembly using HISAT2 (version 2.1.0). Abundance of transcripts was calculated using the default parameters in stringtie2 (version 1.3.4d) and annotation of transcripts were based on ENSEMBL GRCh38.87. Gene count matrices were generated using the \"prepDE.py\" script according to the protocol found in the stringtie2 documentation., , # Data from: Human conjunctival transcriptome in Acanthamoeba keratitis: An exploratory study

[https://doi.org/10.5061/dryad.k3j9kd5fx](https://doi.org/10.5061/dryad.k3j9kd5fx)

## Description of the data and file structure

### List of files

```
ENSG_ID2Name.txt
conj_transcriptome_stringtie2_counts_md5-9660d96d.csv
conj_transcriptome_metadata.csv
```

### Description of data

`ENSG_ID2Name.txt` is a text file containing the mapping of ENSG IDs to gene names.

The CSV file `conj_transcriptome_stringtie2_counts_md5-9660d96d.csv` contains counts for human genes found in 22 conjunctival samples. RNA-Seq data was generated on an Illumina NovaSeq 6000 sequencing machine at the UCSF sequencing center. Sequencing reads were quality filtered using PriceSeqFilter, and aligned to the GRCh38 human genome assembly using HISAT2 (version 2.1.0). Abundance of genes was calculated using the default parameters in stringtie2 (version 1.3.4d). Annotation of transcripts was based on ENSEMBL GRCh38.87. Th...