Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
Project description:Our proteomics data (PXD030253) indicate RNA polymerase II is co-localized with Aldh18a1. To confirm this observation using an orthogonal method we performed ChIP-seq experiments to identify the binding patterns of RNA polymerase II in general, and RNA polymerase II with S2-phosphorylated CTD. We also performed Cut&Run using Aldh18a1 antibody which is submitted separately. To do a ChIP-seq, mES cells (46C) were treated with Accutase to be detached. The cells were fixed by 1.5% formaldehyde in PBS for 15min. Chromatin was fragmented by sonication and sheared to < 500 bp fragments. The cell debris were removed by spinning. The sheared chromatin was treated with 10 ug antibodies (pan-Pol II Bethyl A304-405A, or S2P-Pol II Bethyl A304-407A) overnight at 4 °C. Dynabeads protein A beads (40ul) were added to the samples and the samples were rotated 2-3 hours to perform the immunoprecipitation. The beads were washed 5 times. Chromatin was eluted in a denaturing solution, and proteins were digested using proteinase K. DNA was purified by SPRI beads. The ChIP libraries were prepared using NEBNext Ultra II DNA library prep according to the manufacturer manual. The libraries were sequenced using 150nt reads on paired-end mode by HiSeq4000. Reads were trimmed, aligned to the mouse genome (mm10) using Bowtie2, and duplicated reads were removed with samtools. The ChIP quality was evaluated by cross-correlation using the “SPP'' tool as suggested by ENCODE ChIP-seq guidelines. Peak calling was performed using MACS2.
Project description:This research reports genome-wide measurements of genetic and epigenetic patterns of inheritance through an integrative analysis of BS-seq, RNA-seq, and siRNA-seq data in two inbred parents of the Nipponbare (NPB) and Indica (93-11) variety of rice and their hybrid offspring. We generated integrative maps of whole genome cytosine methylation profiles (BS-Seq), transcriptional profiles (RNA-seq), and small RNA profiles (sRNA-seq) to characterize two rice subspecies, Oryza sativa spp japonica (Nipponbare) and Oryza sativa spp indica (93-11) and their two reciprocal hybrid offspring using Illumina's sequencing-by-synthesis (SBS) platform .
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels
Project description:RNA-Seq libraries from Arabidopsis thaliana seedlings