Project description:Homo sapiens fresh whole blood was infected with Candida parapsilosis. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Homo sapiens gene expression.
Project description:Homo sapiens fresh whole blood was infected with Candida albicans SC5314. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
Project description:Experiment with 32 hybridizations, using 16 samples of species [Homo sapiens], using 32 arrays of array design [Affymetrix Custom Array - NuGO_Hs1a520180], producing 32 raw data files and 1 transformed and/or normalized data files.
Project description:Experiment with 6 hybridizations, using 30 samples of species [Homo sapiens], using 6 arrays of array design [Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]], producing 6 raw data files and 6 transformed and/or normalized data files.
Project description:Five HCMV (+) CRC tissues detected by PCR were selected for RNA-seq. GEPs were pre-processed by Cutadapter and FastQC to remove jointed reads and low-quality reads. Tophat (v.2.0.0) was used to compare the sequences with Homo sapiens and HCMV genomes. The GEPs of HCMV was determined by Integrated Genomics Viewer (IGV) and Partek® Genomics Suite™ (version 6.5 beta, Partek Inc., St. Louis, MO, USA).
Project description:Search for SNPs associated with the pharmacogenomic profile of Benzidazole adverse reactions in Chagas Disease Homo sapiens patients.
Project description:Expression analysis of gene expression changes in Homo sapiens SGC-7901 cells after knock down of MTA2 (Metastasis-associated protein) or overexpression SNHG5 (snoRNA host gene 5) Investigation of whole genome gene expression level changes in a Homo sapiens gastric carcinoma cells SGC-7901 after knock down MTA2 expression and upregulation of SNHG5
Project description:We report the results of performing RNA sequencing using RNA extracted from TC28a2 cells grown in the presence of hypertrophic differentiation medium compared to RNA extracted from TC28a2 cells grown in growth medium. For preparation of samples for RNA sequencing, total RNAs were extracted from TC28a2 cells treated with growth medium (n=2) or hypertrophic medium (n=3) at day 5 of differentiation. RNA was extracted using Trizol (Invitrogen) following the protocols provided by the manufacturer. Isolated RNAs were submitted to the Macrogen Inc. (Macrogen Inc., Seoul, South Korea) for total RNA-sequencing. The overall quality of the extracted total RNAs were validated using spectrophotometry. To remove low quality and adapter sequence, the raw was read by the sequencer before analysis and align the processed reads to the Homo sapiens using HISAT2 v2.1.059. The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from the NCBI, and transcript assembly of known transcripts was then processed by StringTie v2.1. Base on the result of that, expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample. The expression profiles are used to do additional analysis such as DEG (Differentially Expressed Genes). The relative abundances of gene were measured in read count using StringTie. Genes with one more than zeroed read count values in the samples were excluded. Filtered data were log2-transformed and subjected to RLE Normalization. Statistical significance of the differential expression data was determined using DESeq2 nbinomWaldTest and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm. For DEG set, hierarchical clustering analysis was performed using complete linkage and Euclidean distance as a measure of similarity. Enrichment of gene ontology analysis was performed for DEGs using g:Profiler and KEGG pathway analysis was tested based on KEGG pathway (https://www.genome.jp/kegg/) database. We used multidimensional scaling (MDS) method to visualize the similarities among samples. We applied to the Euclidean distance as the measure of the dissimilarity. Hierarchical clustering analysis also was performed using complete linkage and Euclidean distance as a measure of similarity to display the expression patterns of differentially expressed transcripts which are satisfied with fold change ≥2 and raw p <0.05. All data analysis and visualization of differentially expressed genes was conducted using R 3.6.1(www.r-project.org).
