Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic analysis of a moderately growing subisolate Botryococcus braunii 779 (Chlorophyta) in response to nitrogen deprivation

ABSTRACT: We report the transcriptomic response of a moderately growing subisolate from the culture of Botryococcus sp. CCALA-779 upon nitrogen deprivation (ND). Examination of transcriptomes upon nitrogen deprivation (ND). B.braunii_non_redundant_transcriptome_assembly_61220.fasta: non-redundant assembly (with 61220 in number) of B.braunii 779 transcriptome in this study B.braunii_annotated_12292.fasta: investigated ESTs (with 12292 in number, which perfectly matches with our processed RNA expression profiling) in this study

ORGANISM(S): Botryococcus braunii

SUBMITTER: Jianhua Liu

PROVIDER: E-GEOD-71296 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic analysis of a moderately growing subisolate Botryococcus braunii 779 (Chlorophyta) in response to nitrogen deprivation

Project description:We report the transcriptomic response of a moderately growing subisolate from the culture of Botryococcus sp. CCALA-779 upon nitrogen deprivation (ND).

2015-08-03 | GSE71296 | GEO

Analysis of proteome refines key molecular reprogramming mechanisms during oil production in Nannochloropsis oceanica

Project description:To examine the mechanisms during oil production and integrate analysis of lactylation in N. oceanica, protein expression profiles were tracked after nitrogen deprivation for three days using 4D label-free proteome method. Under nitrogen deprivation (ND) and nitrogen repletion (NR) cultivation conditions, we mapped proteome of proliferating microalgal cells.

2024-07-03 | PXD038833 | Pride

Analysis of lactylome refines key molecular reprogramming mechanisms during oil production in Nannochloropsis oceanica

Project description:Lysine lactylation as a type of posttranslational modifications (PTMs) is recently associated with chromatin remodeling and gene transcription, but lysine lactylation of histone and non-histone proteins has not yet been studied in Nannochloropsis oceanica. To examine the prevalence and function of lactylation in N. oceanica, protein lactylation modification profiles were tracked after nitrogen deprivation for three days using 4D label-free proteome method. Under nitrogen deprivation (ND) and nitrogen repletion (NR) cultivation conditions, we mapped lactylome of proliferating microalgal cells.

2024-07-03 | PXD038775 | Pride

The identification of adenylyl cyclase modulators as potential receptors for 6-nitrodopamine in human-induced pluripotent stem cell (hiPSC)-derived cardiomyocytes and their relevance in heart inotropism

Project description:6-Nitrodopamine Q7 Q8 (6-ND Q9 ) has potent positive chronotropic and inotropic effects. At a very low dose, i.e., 10 fM, it causes potentiation of the positive chronotropic effects induced by catecholamines in the rat atria, indicating a distinct mechanism of action. Cyclase-associated proteins (CAP-1 and CAP-2) are potential receptors for 6-ND in human cardiomyocytes. Since cyclic 3′,5′-cyclic adenosine monophosphate (cAMP) plays a fundamental role in the positive inotropic effects of classical catecholamines, it was further investigated whether 6-ND potentiates the positive inotropic effects induced by classical catecholamines in the rat isolated perfused heart. Human-induced pluripotent stem cell (hiPSC)- derived cardiomyocytes were harvested and lysed, and following appropriate separation procedures, membrane proteins were incubated with 6-NDderivatized agarose, centrifuged, and the proteins retained in the agarose eluted with 6-ND (1 mM). The proteins isolated from the chemical pulldown assay were fractionated by SDS-PAGE, the bands were cut and hydrolyzed in situ with trypsin, and then separated and sequenced. A total of 817 proteins were generated, and following screening using UniProt “Retrieve/ID Mapping” function and Gene Ontology cellular component category, 124 proteins were identified as membrane proteins. These experiments identified three proteins that modulate adenylyl cyclase (AC) activity (CAP-1, CAP-2, and STIM1), which are compatible with the pharmacological findings reported for 6-ND in the rat heart. As expected, 6-ND strongly potentiates the inotropic effect induced by noradrenaline in Langendorff’s preparation. In conclusion, 6-ND-induced potentiation of catecholamine-induced chronotropic and inotropic effects is due to the modulation of adenylyl cyclase activity, probably via direct interactions with CAP-1 and CAP-2.

2025-09-08 | PXD066711 | Pride

Change in gene expression of a canine melanoma cell line caused by exposure to nonsteroidal anti-inflammatory drugs (NSAIDs) .

Project description:Nonsteroidal anti-inflammatory drugs (NSAIDs) has been suggested as adjunctive anti-tumor agents in human and veterinary medicine. However, its anti-tumor molecular machinery is still controversial. Therefore, we performed whole transcriptome analysis to discover gene expression influenced by NSAIDs treatment. A canine melanoma cell line (Mi/CMM1) was treated by three NSAIDs, piroxicam, carprofen, and robenacoxib, at their half maximal (50%) inhibitory concentrations (116 ÂµM, 779 ÂµM, and 156 ÂµM) for 6 hours. Subsequently, total RNA were extracted and microarray analysis was performed to evaluate change in gene expression caused by NSAIDs treatment. Each condition had three biological replicates.

2016-03-09 | E-GEOD-78988 | biostudies-arrayexpress

Transcriptomic and lipidomic analysis of an EPA-containing Nannochloropsis sp. PJ12 in response to nitrogen deprivation

Project description:Oleaginous microalgae Nannochloropsis spp. are considered to be promissing species for production of biofuels and biomaterials. Nevertheless, its biofuel production remains to be economically unviable. Hence, further improvement of cultivation conditions and genetic traits for high-lipid contents without affecting growth is required. To understand genes involved in neutral lipid accumulation upon nitrogen deprivation (ND) in a novel isolate of Nannochloropsis sp. PJ12, we performed comparative transcriptomic and lipidomic analyses of cells under ND and NR (nitrogen replete) conditions. Transcriptomic profiling indicated that, while enzymes involved in TCA cycle in PJ12 under ND condition were upregulated compared to that under NR condition, those involved in Calvin cycle and glycolysis under ND condition were downregulated, consistent with the observation that quantum yield was reduced under ND condition. Furthermore, we showed that enzymes involved in fatty acid synthesis and glycerolipid synthesis were downregulated but not b-oxidation. Lipidomic profiling indicated that, while the level of neutral lipids in ND cells was increased compared to that of NR cells, level of photosynthetic membrane-lipids DGDG and MGDG was decreased. Taken together, our analysis indicated that TAG accumulation is attributed to the modification of membrane lipids derived primarily from “prokaryotic” pathway and secondarily from “eukaryotic” pathway based on the 16:X or 18:X fatty acid at the sn2 position of the glycerol backbone. We propose that two-phase (NR-ND) growth is ideal for biomass and biofuel production because ND reduces cell growth rate due to the loss of photosynthetic membrane and decreased quantum yield.

2019-03-20 | GSE118760 | GEO

Single-cell RNA-seq of wild-type and Pbx1/Pbx2 double-knockout EpiSCs differentiated in vitro to pre-somitic mesoderm in the first 48 hours of differentiation.

Project description:In vertebrates, body axis elongation is fuelled by bipotent neuromesodermal progenitors (NMPs), which support the development of both spinal cord and paraxial mesoderm (PM). HOX transcription factors have been historically implicated in axial elongation, with their sequential activation playing a fundamental role in timing PM development. PBX1 and PBX2 are obligate anterior HOX cofactors, and therefore they represent prominent candidates for controlling the distinct response to individual HOX factors. To pinpoint the role of PBX proteins in the development of pre-somitic mesoderm (PSM), wild-type (WT) and Pbx1/Pbx2 double-mutant (Pbx1/2-DKO) EpiSCs were differentiated in vitro to PSM. Single cells from different time-points (WT: EpiSCs, 6 hours, 12 hours, 24 hours, 36 hours, 48 hours; Pbx1/2-DKO: 24 hours, 36 hours, 48 hours) were FACS-sorted into 384-well capture plates, and single-cell RNA-sequencing was performed using MARS-seq (Jaitin D.A. et al., Science, 343, 776-779 (2014)). Two wells were left empty in each plate, as a no-cell control during data analysis.

2021-07-21 | E-MTAB-9774 | biostudies-arrayexpress

Integration of epigenome and lactylome reveals the regulation of lipid production in Nannochloropsis oceanica [RNA-Seq]

Project description:Lysine lactylation (Kla) is a kind of novel post-translational modification (PTM), which participates in gene expression and various metabolic processes. Nannochloropsis, a significant oleaginous microalgae of economic significance, demonstrates a remarkable capacity for triacylglycerol (TAG) production under nitrogen stress. To elucidate the involvement of lactylation in lipid synthesis, we conducted ChIP-seq and mRNA-seq analyses to monitor lactylation modifications and transcriptome alterations in Nannochloropsis oceanica. In all, 2,057 genes showed considerable variation between nitrogen deprivation (ND) and nitrogen repletion (NR) conditions, comprising 853 upregulated genes and 1,204 downregulated genes. Moreover, a total of 5,375 differential Kla peaks were identified, including 5,331 gain peaks and 44 loss peaks under ND vs NR. The differential Kla peaks were primarily distributed in the promoter (<= 1 kb) (71.07%), 5’UTR (22.64%), and exon (4.25%). Integrative analysis of ChIP-seq, transcriptome, and previous proteome and lactylome data elucidates the potential mechanism by which lactylation promotes lipid accumulation under ND. Lactylation facilitates autophagy and protein degradation, leading to the recycling of carbon into the tricarboxylic acid (TCA) cycle, thereby providing carbon precursors for lipid synthesis. Additionally, lactylation induces the redirection of carbon from membrane lipids to TAG by upregulating lipases and enhancing the TCA cycle and β-oxidation pathways. This research reveals the regulatory functions of lactylation in lipid metabolism and gene expression in Nannochloropsis, offering a new perspective for the investigation of lipid biosynthesis.

2024-06-26 | GSE260894 | GEO

Integration of epigenome and lactylome reveals the regulation of lipid production in Nannochloropsis oceanica

2024-06-26 | GSE261019 | GEO

Single-cell RNA-seq of tailbuds from control, Pbx1/Pbx2 compound and Pbx1/Pbx2 double-knockout E8.5/E9.0 embryos.

Project description:In vertebrates, body axis elongation is fuelled by bipotent neuromesodermal progenitors (NMPs), which support the development of both spinal cord and paraxial mesoderm (PM). NMPs reside in the caudal lateral epiblast and tailbud, from where they sustain axial elongation. HOX transcription factors have been historically implicated in axial elongation, with their sequential activation playing a fundamental role in timing PM development. PBX1 and PBX2 are obligate anterior HOX cofactors, and therefore they represent prominent candidates for controlling the distinct response to individual HOX factors. To pinpoint the role of PBX proteins in the development of pre-somitic mesoderm, single-cell RNA sequencing (scRNA-seq) was performed on cells isolated from the tailbuds of control, Pbx1/Pbx2 compound (Pbx1/2-com) and Pbx1/Pbx2 double-mutant (Pbx1/2-DKO) embryos at embryonic days 8.5 and 9.0. Single cells from at least three embryos per genotype and stage were FACS-sorted into 384-well capture plates, and scRNA-seq was performed using MARS-seq (Jaitin D.A. et al., Science, 343, 776-779 (2014)). As a spike-in internal control for batch-effect correction, 71 EpiSCs cultivated in vitro were sorted into each plate, together with 311 cells from embryonic tailbuds. Two wells were left empty in each plate, as a no-cell control during data analysis.

2021-07-21 | E-MTAB-9785 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data