Project description:Here we show that epithelial BRG1, the catalytic subunit of SWI/SNF complex is critical for colitis and colitis-associated-cancer. Depletion of BRG1 in colonrectal epithelial cells make mice develop Spontaneous colitis. To dissect underlying mechanism, we conducted gene expression profile analysis (RNA-Seq) by using primary colonrectal epithelial cells isolated from BRG1CTRL and BRG1IEC-KO(Tamoxifen induced BRG1 knock-out) mice to gain molecular insights into the affected biological processes. To this end, colorectal epithelial cells were isolated after 7 days of tamoxifen treatment, on which day BRG1-depleted mice showed little morphological defects in colon in comparison with control littermates. IECs were isolated by EDTA isolation buffer. Each sample contains pooled mRNA from 3 mice, and was subjected to Hiseq RNA-Seq, performed by Guangzhou RiboBio Co., Ltd. (Guangzhou, China)using IlluminaHiSeq 3000 platform.
Project description:Purpose: To reveal the global regulatory genes of clinical strain, we performed comparative transcriptomic analyses of the SC5314 and JL01.Methods: We isolated a clinical Candida albicans strain JL01 (Jinling Hospital in Nanjing, China) from a 21-year-old man who presented to our hospital with recurrent cervical lymphadenitis. Cells of the JL01 and SC5314 were inoculated from overnight cultures by 1% into liquid YPD plus 10% serum medium at 37°C for 3 h. Cells were collected and total RNA was extracted as described. RNA-Seq analysis was performed by the company Majorbio (Shanghai, China). mRNA was purified, fragmented and used to synthesize cDNA. The library products were sequenced on the HiSeq 4000 platform using the HisSeq 4000 PE Cluster Kit and HisSeq 4000 SBS Kit.Results: 421 genes were significantly differentially regulated (P≤0.05, |log2FC|≥1) in JL01 compared with SC5314. Of these 421 DEGs (differentially expressed genes), 216 were up-regulated, and 205 were down-regulated. Conclusions: Together the clinical, morphological and biological analyses, we suggest that azole drug resistance, invasive defect and hypo-virulence of the JL01 strain may correlate with its contribution in chronic fungal infection.
Project description:Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, RP China
Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, RP China
Project description:In this study, two multiantibiotic-resistant bacteria, Ochrobactrum intermedium (N1) and Stenotrophomonas acidaminiphila (N2), were isolated from the sludge of a PWWTP in Guangzhou, China. Whole-genome sequencing revealed that N1 and N2 had genome sizes of 0.52 Mb and 0.37 Mb, respectively, and harbored 33 and 24 ARGs, respectively. The main resistance mechanism in the identified ARGs included efflux pumps, enzymatic degradation, and target bypass, with the N1 strain possessing more multidrug-resistant efflux pumps than the N2 strain (22 vs 12). This also accounts for the broader resistance spectrum of N1 than of N2 in antimicrobial susceptibility tests. Additionally, both genomes contain numerous mobile genetic elements (89 and 21 genes, respectively) and virulence factors (276 and 250 factors, respectively), suggesting their potential for horizontal transfer and pathogenicity.
Project description:The purpose of this study is to analysis 41 RNA modification enzymes in 1659 HBM samples from 10 public datasets, and 100 HCC samples from Zhongshan Hospital of Fudan University (Shanghai, China). we designed an RH score model to predict the clinical prognosis, response to molecular targeted drugs and immunotherapy and transcriptional and posttranscriptional events, thereby providing a novel panel of next-generation sequencing for clinical translation.
2023-04-26 | GSE222334 | GEO
Project description:Guangzhou, Guangdong, China KP-ST11
Project description:We found that a novel gene Gm614 mRNA significantly changed in plasma cells. Because of plasmablast-like, Mus musculus myeloma SP 2/0 cell line was selected to test the effect of Gm614 overexpression on plasmablast/plasma cells. Gm614 cDNA (General Biosystems, Anhui, China) was cloned into lentiviral vector LV201 (Fugene Corp., Guangzhou, China) to generate Gm614 protein. Gm614-expressing LV201 was then transfected into SP 2/0 cells, and stable transfectants were identified by drug selection (Puromycin, Sigma, 10 μg/ml). To identify the effect of Gm614 overexpression on gene expression, we determined mRNA profiles in Gm614-overexpressed and vector-transduced SP 2/0 cells by RNA-seq. RNA-seq was done with an Illumina HiSeq 2500 instrument at GENEWIZ, Suzhou, China.
Project description:Total RNAs from exosomes was used for miRNA library preparation and sequencing.The preparation and sequencing of exosome miRNA were performed by Ribobio (Guangzhou, China). First, total RNA samples were fractionated by using 15% Tris-borate-EDTA (TBE) polyacrylamide gel (Invitrogen), then small RNAs ranging from 18 to 30 nucleotides were used for library preparation. Amplification of these small RNAs was then accomplished by PCR. Next, the Illumina HiSeq 2500 platform was used to sequence these RNAs.
Project description:Total RNA was extracted from WT and RBP-JCKO mBMDMs at 36 hpi (HTMV, MOI=1), using TRIzol (Invitrogen). Ribosomal RNA was removed using the Ribo-Zero™ kit (Epicentre Biotechnologies). Fragmented RNA (the average length was approximately 200 bp) was subjected to first-strand and second-strand cDNA synthesis followed by adaptor ligation and enrichment with a low cycle according to the instructions of the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0 (Life Technologies). The libraries were paired-end sequenced (PE150, sequencing reads were 150 bp) at Guangzhou Ribo Biotechnology (Guangzhou, China) using the Illumina HiSeq 3000 platform. Transgenic mice type: RBP-JCKO (Lyz2-Cre+ RBP-Jfloxed) C57BL/6J Mice.
