Project description:To gain insight into the gene signatures directly mediated by LAP (CEBPB) for cancer cell progression, we performed RNA-seq in LAP-HepG2 versus control cells.
Project description:To identify differentially expressed genes between apatinib-sensitive and apatinib-resistant HUVECs, one apatinib-sensitive and one -resistant primary human umbilical vein endothelial cells (HUVECs) were treated with apatinib for 48 hours. After treatment, cells were harvested and total RNA was extracted. The quantity and integrity of the RNA were evaluated and sequencing libraries were constructed.
Project description:In this study, we make used of mRNA-seq and its ability to reliably quantify isoforms, integrating this data with ribosome profiling and LC-MS/MS, to assign ribosome footprints and peptides at the isoform level. We leverage the principle that most cell types, and even tissues, predominantly express a single principal isoform to set isoform-level mRNA-seq quantifications as priors to guide and improve allocation of footprints or peptides to isoforms. Through tightly integrated mRNAseq, ribosome footprinting and/or LC-MS/MS proteomics we demonstrate that a principal isoform can be identified in over 80% of gene products in homogenous HEK293 cell culture and over 70% of proteins detected in complex human brain tissue. Defining isoforms in experiments with matched RNA-seq and translatomic/proteomic data increases the functional relevance of such datasets and will further broaden our understanding of multi-level control of gene expression. In this PRIDE submission you will find the raw files for the HEK293 cell proteomics. Files for the human brain proteomics can be found at PXD005445. We have also uploaded a zip file that contains the input files for our HEK293 cell analysis, and the isoform level output files – there is a separate folder within the zip files for these. The data used to create the manuscript figures is in the Rdata file. Code for assigning peptides and footprints to isoforms can be found on Github here: https://github.com/rkitchen/EMpire
Project description:Acute hemolysis can deplete haptoglobin and hemopexin, leaving toxic free heme insufficiently controlled. Here, the authors show that scavenger receptor BI (SR-BI) mediates hepatic uptake of free heme and is essential for protection against heme-induced injury and death. Here we examined gene expression post hemin injections
Project description:The goals of this study are to compare differential gene expressions for Penicillium oxalicum wild type strain (WT), and laeA knockout strain (ΔlaeA) in different development phase. The deletion of laeA downregulated genes involved in oxidation- reduction process, alkaloid metabolic process, and transmembrane transport. We find the expression levels of seven secondary metabolism gene clusters (totally 28 clusters) were silenced inΔlaeA. This study provides the information that laeA function are required in conidiation and hydrolase activity of P. oxalicum. Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and laeA knockout mutant strains in 24h and 60h in modified Czapek culture medium with 2% glucose as carbon resource. qRT–PCR validation was performed using SYBR Green assays.
Project description:microRNA transcriptome data from wild type and Gata6-deficient tissue resident peritoneal macrophages. Tissue resident macrophages are notoriously heterogeneous, exhibiting discrete phenotypes as a consequence of tissue- and micro-anatomical niche-specific functions, but the molecular basis for this is not understood. Gata6 itself has been shown to be a target of multiple miR. However, microRNA transcriptome and its dependence on tissue-specific macrophage programming, such as effected by GATA6, has not been explored. We used microRNA sequencing to determine the patterns of microRNA expression in peritoneal resident macrophages at homeostasis in the absence of GATA-6 against wild type.
Project description:Transcriptomic analysis of fungus Penicillium decumbens and brlA deletion strains in liquid medium and solid medium respectivelly Examination of differential gene expressions by Penicillium decumbens strains 114-2 and brlA deletion stains in liquid medium and solid medium
Project description:Growth failure is a major complication of pediatric inflammatory bowel disease (IBD), a condition whose prevalence has risen sharply over recent decades. Despite advances in medical therapy, linear growth impairment often persists. This underscores the urgent need to elucidate how chronic inflammation disrupts skeletal development at the epiphyseal growth plate (EGP), the central driver of longitudinal bone growth. Our study proposes a novel mechanism, involving the activation of ELANE, a serine proteinase previously shown to be secreted by neutrophils in response to inflammatory stimuli. We report for the first time that EGP chondrocytes express ELANE, with significant upregulation observed in DSS-induced colitis and in ATDC5 cells exposed to LPS. The concomitant induction of ELANE and MMP13 indicates a direct catabolic effect on the extracellular matrix, leading to impaired growth plate function. While ELANE is well established in cartilage degradation and bone remodeling in rheumatoid arthritis and osteoarthritis, its expression in the EGP and its role in growth impairment during IBD represent novel findings. These findings open new perspectives on inflammation-driven growth impairment in pediatric IBD, highlight ELANE as a promising therapeutic target to preserve skeletal development.
Project description:Lead Exposure and Human Brain Evolution: A 2-Million-Year Perspective This study reveals that lead exposure was pervasive throughout human evolution, not just a modern phenomenon. Researchers analyzed 51 fossil teeth from multiple hominid species spanning 2+ million years across three continents, finding lead exposure evidence in 73% of specimens using advanced laser ablation mass spectrometry. The team then used human brain organoids carrying either modern or archaic (Neanderthal-like) variants of the NOVA1 gene to test lead's neurological impacts. They discovered that the archaic variant showed greater vulnerability to lead-induced disruption of FOXP2 expression—a gene crucial for speech and language development. This suggests environmental lead exposure may have created evolutionary pressure favoring the modern human NOVA1 variant, potentially giving our species advantages in communication and social cohesion. The research challenges established paradigms about both environmental toxin history and human evolution, proposing that gene-environment interactions with neurotoxins helped shape our species' cognitive development over millions of years.