RNAseq SysMetEx
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB30001 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Targeted single-cell RNAseq of tonsil organoid cultures
| PRJNA665262 | ENA
Project description:Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities. Using a dual RNA-seq approach, we describe the first study of the transcriptional responses of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw. Based on quantification of species-specific rRNA, a set of conditions was identified where mixed cultures could be sampled so as to obtain sufficient RNA-seq reads for analysis from each species. The number of differentially-expressed genes varied from a couple of thousand to fewer than one hundred. The proportion of carbohydrate active enzyme (CAZy) encoding transcripts was lower in the majority of the mixed cultures compared to the respective straw monocultures. A small subset of P. chrysogenum CAZy genes showed five to ten-fold significantly increased transcript abundance in a two-species mixed culture with T. reesei. However, a substantial number of T. reesei CAZy transcripts showed reduced abundance in mixed cultures. The highly induced genes in mixed cultures indicated that fungal antagonism was a major part of the mixed cultures. In line with this, secondary metabolite producing gene clusters showed increased transcript abundance in mixed cultures and also mixed cultures with T. reesei led to a decrease in the mycelial biomass of A. niger. Significantly higher monomeric sugar release from straw was only measured using a minority of the mixed culture filtrates and there was no overall improvement. This study demonstrates fungal interaction with changes in transcripts, enzyme activities and biomass in the mixed cultures and whilst there were minor beneficial effects for CAZy transcripts and activities, the competitive interaction between T. reesei and the other fungi was the most prominent feature of this study.
2016-05-07 | GSE81187 | GEO
Project description:Single cell RNAseq was performed on PBMC isolated from health workers who received two doses of Pfizer COVID19 vaccine and determined as either normal responders or low responders by antibody test. Each group has 4 patients. Cells from each patient were labeled with Totalseq C hashing antibodies and mixed 1:1:1:1 for each group. Single cells were further captured using 10x chromium Next GEM 5 prime kit.
2022-10-03 | GSE199123 | GEO
Project description:Biofilm formation by Escherichia coli was significantly inhibited when co-cultured with Stenotrophomonas maltophilia in static systems. Genes of E. coli involved in species interactions with S. maltophilia were identified in order to allow the study of the mechanisms of inhibited E. coli biofilm formation in co-culture. A total of 89 and 108 genes were identified as differentially expressed in mixed species cultures when growing as biofilm and as planktonic cultures, respectively, compared to the counterpart of pure cultured E. coli. Differential expression of certain identified genes was confirmed using E. coli reporter strains combined with single-cell based flow cytometry analysis. Co-culture with S. maltophilia affected genes involved in metabolism, signal transduction, cell wall composition, and biofilm formation of E. coli. Several selected genes were further confirmed as affecting E. coli biofilm formation in mixed species cultures with S. maltophilia. The data suggest that these genes were involved in species interactions between E. coli and S. maltophilia. This SuperSeries is composed of the SubSeries listed below.
2013-12-30 | GSE24915 | GEO
Project description:Escherichia coli planktonic cultures: mono-species culture vs. mixed-species culture
| PRJNA133405 | ENA
Project description:Ba/F3 cells were transformed after transfection with CRISPR/CAS9 + gRNA vs target gene. Oligoclonal cell population was flow sorted into single cells and processes for RNAseq.
2014-12-09 | E-ERAD-298 | biostudies-arrayexpress
Project description:Autophagy is an evolutionary ancient mechanism that sequesters substrates for degradation within autolysosomes. The process is driven by many autophagy-related (ATG) proteins, including the core members ATG9 and ATG16. Here, we applied RNAseq and tandem mass tag (TMT) proteomic approaches to identify differentially expressed genes (DEGs) and proteins (DEPs) in ATG9‾, ATG16‾ and ATG9‾/16‾ strains in comparison to AX2 wild-type cells. In total, we identified 332 (279 up and 53 down), 639 (487 up and 152 down) and 260 (114 up and 146 down) DEGs and 124 (83 up and 41 down), 431 (238 up and 193 down) and 677 (347 up and 330 down) DEPs in ATG9‾, ATG16‾ and ATG9‾/16‾ strains, respectively. Thus, in the single knock-out strains, the number of DEGs was higher than the number of DEPs while in the double knock-out strain the number of DEPs was higher. Comparison of RNAseq and proteomic data further revealed, that only a small proportion of the transcriptional changes were reflected on the protein level. This suggests that most changes in protein abundance were not caused by transcriptional changes but were rather due to changes in protein homeostasis. Gene ontology (GO) analysis revealed an enrichment of DEPs involved in lipid metabolism and oxidative phosphorylation. Furthermore, we found increased expression of the anti-oxidant enzymes glutathione reductase (gsr) and catalase A (catA) in ATG16‾ and ATG9‾/16‾ cells, respectively, indicating adaptation to excess reactive oxygen species (ROS). Our study provides the first combined transcriptome and proteome analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells and adds to our knowledge of functions of these proteins.
2021-06-15 | PXD023730 | Pride
Project description:To determine transcriptome differences in Vibrio cholerae when grown as planktonic and biofilm cultures, whole-genome level transcriptional profiling was performed using RNAseq analysis. Transcriptomes of biofim and planktonic cultures were compared in this study.
2020-05-28 | GSE135887 | GEO
Project description:Single nucleus RNAseq of cerebellar nucleus neurons in three species
| PRJNA673247 | ENA
Project description:To explain enhanced biofilm formation and increased dissemination of S. epidermidis in mixed-species biofilms, microarrays were used to explore differential gene expression of S. epidermidis in mixed-species biofilms. One sample from single species biofilm (S1) and mixed-species biofilm (SC2) were excluded from analyses for outliers. We observed upregulation (2.7%) and down regulation (6%) of S. epidermidis genes in mixed-species biofilms. Autolysis repressors lrgA and lrgB were down regulated 36-fold and 27-fold respectively and was associated with increased eDNA possibly due to enhanced autolysis in mixed-species biofilms. These data suggest that bacterial autolysis and release of eDNA in the biofilm matrix may be responsible for enhancement and dissemination of mixed-species biofilms of S. epidermidis and C. albicans. Staphylococcal gene expression in mixed-species biofilms with Candida and in single species biofilms of S. epidermidis were analyzed. The experiment was repeated thrice on 3 different days (3 biological replicates each for single species biofilms of S. epidermidis and mixed-species biofilms). Only 2 biological replicates were analyzed and one biological replicate was not analyzed (S1 and SC1 - raw data files are provided on the Series record). Single species biofilms of S. epidermidis (strain 1457) and C. albicans (strain 32354) and mixed-species biofilms were formed on 6-well tissue culture plates. Five ml of organism suspensions (O.D. 0.3, S. epidermidis 107 CFU/ml or C. albicans 105 CFU/ml) or 2.5 ml each for mixed-species biofilms for 24 hr. RNA was harvested from single species and mixed-species biofilms.
2012-02-28 | E-GEOD-35438 | biostudies-arrayexpress