Project description:Analysis of leaves of wild-type and rice COI mutants treated with methyl jasmonate (MeJA). Results provide the role of rice COI on response to jasmonic acid.
Project description:This study is to investigate the effects of glycellin I (GI) and glyceollin II (GII), a aryl hydorcarbon (AhR) ligand in genome. Cells were treated during 24h with glyceollins alone or in combination with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Total RNA was prepared and controlled the quality. Total RNA was prepared and controlled the quality. Then, a 3’Digital Gene Expression (DGE) library was constructed using a modified SCRB-Seq protocol [55] with barcoded poly-dT RT primers and a hybrid Nextera/TruSeq sequencing strategy. Data quality control and data preprocessing were performed by the GenoBiRD Platform in Nantes, France. The results showed that there are numerous gene regulated by TCDD are also modified by GI or GII. GI et GII can have antagonistic or synergistic effects together with TCDD. This is the first study elucidating the effect of GI and GII in three cell types. Method: Cells were treated during 24h with glyceollins alone or in combination with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Total RNA was prepared and controlled the quality. Total RNA was prepared and controlled the quality. Then, a high-Throughput mRNASeq library for 3’Digital Gene Expression (DGE) was constructed using a modified SCRB-Seq protocol [55] with barcoded poly-dT RT primers and a hybrid Nextera/TruSeq sequencing strategy. Data quality control and primary analysis were performed by the GenoBiRD Platform in Nantes, France.
Project description:Stem cell-based therapies show promise as a means of repairing the degenerate intervertebral disc, with growth factors often used alongside cells to help direct differentiation towards a nucleus pulposus (NP)-like phenotype. We previously demonstrated adipose-derived stem cell (ASCs) differentiation with GDF6 as optimal for generating NP-like cells through evaluating end-stage differentiation parameters. Here we conducted a time-resolved transcriptomic characterisation of ASCs response to GDF6 stimulation to understand the early drivers of differentiation to NP-like cells.
Project description:We provided an improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor. We valided the strategy by characterzing the DNA-binding specificty of NF-M-NM-:B p50 dimer. Proteins of the Nf-kappab family were bound to DNA oligonucleotides containing a degenerate region. The protein-DNA complexes were selected after one or multiple rounds of SELEX and the DNA molecules were deep sequenced.
Project description:Aim: To improve risk stratification in patients with stable coronary artery disease (CAD), we aimed to identify genes in monocytes predictive of new ischemic events in patients with CAD and determine to what extent expression of these transcripts resembles expression in acute myocardial infarction (AMI). Results: COX10 and ZNF484 distinguished between AMI and the whole group of stable CAD patients with an accuracy of 90%. COX10 and ZNF484 together with MT-COI and WNK1 distinguished AMI patients from stable CAD patients with and without a new event with a sensitivity of 89% and a specificity of 98%. MT-COI and COX10 increased the accuracy for separating stable CAD patients with and without a new coronary event from 68 to 80% in addition to age, gender, BMI, diabetes, lipids, blood pressure and hs-CRP. Interestingly, expression of MT-COI, COX10 and WNK1 (but not ZNF484) in PBMCs paired with that in monocytes; COX10 in whole blood was similar to that in monocytes. Conclusions: This work showed that COX10 and ZNF484, eventually combined with MT-COI and WNK1 have the potential to accurately discriminate between AMI and stable CAD patients, and may improve the risk assessment of stable CAD patients.
2019-08-13 | GSE129935 | GEO
Project description:Evaluating the laboratory flume microbiome as a window into natural hyporheic zone biogeochemistry
Project description:We describe a novel quantitative cDNA expression profiling strategy, involving amplification of the majority of mouse transcriptome using a defined set of 44 heptamer primers. The amplification protocol allows for efficient amplification from as low as 50pg of mRNA and did not alter the expression of the transcripts even with 200 fold dilution of the minimum requirement of the starting material (10ng of mRNA) for standard RNA-seq protocols. We implemented our methodology on embryological lineage segregation, achieved by graded activation of Activin A/TGFβ signaling in mouse embryonic stem cells (mESCs). The fold changes in transcript expression were in excellent agreement with quantitative RT-PCR and we observed a dynamic range spanning more than five orders of magnitude in RNA concentration with a reliable estimation of low abundant transcripts. Our transcriptome data identified key lineage markers, while the high sensitivity showed that novel lineage specific transcripts anticipate the differentiation of specific cell types. We compared our strategy with Std. RNA-seq (Mortazavi et al. 2008) and SMART-seq (Ramsköld et al. 2012). We also showed potential of our methodology to suppress the representation of highly expressing ribosomal transcripts.
Project description:DNA replication is a highly regulated cell cycle process that integrates the time that a genome segment replicates in S phase with its transcriptional activity, chromatin structure, and epigenetic state. The overall goal of this project is to define such linkages in maize by exploiting the genetic and genomic resources of this species. We used an updated Repli-seq protocol to profile replication timing in Zea mays B73 root tips and compare it to other methods for profiling replication timing.
2025-04-28 | GSE288800 | GEO
Project description:Genomics-based approaches to ant monitoring in land management: Validation of COI metabarcoding primers