Project description:We observed gene expression difference between different groups after MDA-MB-231 treated with DMSO, 10 μM DAC, 1 μM DEX, or DAC+DEX. Data obtained from high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format. Gene expression of each groups are listed in raw data files. Some different expression genes between two groups are further validated with qRT-PCR.
Project description:20 random DNA barcodes were designed in silico and transfected into PC3 cells. Barcodes were sequenced using Illumina-Miseq technology to find the sequence and their respective copy numbers. Current file contains the raw data of these DNA barcodes in fastq format
Project description:Purpose: Next-generation sequencing (NGS) technology was used to map expression profiles of effector (spleen) and key target tissues (kidney and brain) in mouse model of Systemic Lupus Erythematosus (SLE). Methods: Total RNA was extracted from total brain, total kidney and total spleen using Trizol and mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Paired-end 37-bp mRNA sequencing was performed on Illumina HiSeq2000 platform. Quality of sequencing was assessed using FastQC software. Raw reads in fastq format were collected and aligned to the mouse genome (mm10 version) using STAR 2.6 algorithm. Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package. Results: We defined kidney-specific molecular signatures of the murine lupus transcriptome that mirrors nephritis-specific transcriptome alterations in human SLE. Conclusions: By the use of the mouse kidney-specific transcriptome and through training of a large whole-blood RNA-sequencing dataset of SLE patients, we developed and validated an algorithm that predicts patients with active LN from SLE patients without LN and suggest vigilance in the monitoring of these patients and potential enrollment in LN prevention studies.
Project description:This study investigates transcriptomic changes in human hepatocellular carcinoma (HCC) cell lines (Huh7 and HLF) cultured under different microenvironmental conditions, including 2D monolayer, 3D Inject-Embed, and 3D Mix-Embed cultures. RNA-seq was performed on total RNA using Illumina NovaSeq 6000 with paired-end 150 bp reads. Raw sequencing reads were aligned to the Homo sapiens reference genome (GRCh38/hg38) using STAR, and gene-level quantification was performed using featureCounts. The dataset includes raw FASTQ files and processed count and FPKM matrices for each sample. This resource provides insights into the impact of 3D culture on liver cancer gene expression.
Project description:Metagenomic raw data (reads in FASTQ format) from 24 environmental samples of sewage sludge and cattle slurry subjected to the methane fermentation process
Project description:Purpose:To understand the change in cellular metabolism and function for the overxepression of SCL27A5 in hepatoma cells. Methods:Total RNAs of AdSLC27A5- or AdGFP-infected PLC/PRF/5 cells were extracted using TRIzol (Invitrogen), following the manufacturer’s instructions. RNA-seq and bioinformatic data analysis were performed by Shanghai Novel Bio Ltd. Briefly, strand-specific RNA-seq libraries were prepared using the Total RNA-seq (H/M/R) Library Prep Kit (Vazyme Biotech, Nanjing, China) and were sequenced on a HiSeq X Ten sequencing platform. Raw reads in FASTQ format were subjected to quality control using FastQC. RNA-seq reads were aligned to the reference genome using Bowtie. Uniquely mapped reads were used for further analysis. Gene expression levels are expressed as RPKM (reads per kilobase per million reads) and differences in gene expression were calculated with rSeq. Results:There were 17 genes differentially expressed in AdSLC27A5-infected PLC/PRF/5 cells compare to the GFP control group (fold change >1.5 or < 0.667; FDR < 0.05).
Project description:Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.