Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome analysis using mass spectrometry (MS) in acute shYthdf2-mediated knockdown of cultured RGCs

ABSTRACT: To identify mouse retinal proteomics changes after Ythdf2 knockdown, we extracted the proteomics of E15.5 retina neurons which were cultured and infected with lentiviral shYthdf2 or shCtrl by urea. After using 100 mM TEAB (Sigma) to dilute the urea concentration to less than 2 M in each sample, trypsin (Promega) was then added to digest the proteins overnight at 37 °C. Peptides were further desalted by Strata X C18 SPE column (Phenomenex) and labelled with TMT10plex Mass Tag Labelling kit (Thermo Scientific) according to the manufactural instructions. Finally, the labeled peptides were subjected to HPLC fractionation and LC-MS/MS analysis.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Fugui Niu

LAB HEAD: Shengjian Ji

PROVIDER: PXD017775 | Pride | 2022-04-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Z8164TQ_1.raw	Raw
	Z8164TQ_10.raw	Raw
	Z8164TQ_11.raw	Raw
	Z8164TQ_12.raw	Raw
	Z8164TQ_13.raw	Raw

Items per page:

1 - 5 of 19

Publications

The m6A reader YTHDF2 is a negative regulator for dendrite development and maintenance of retinal ganglion cells.

Niu Fugui F Han Peng P Zhang Jian J She Yuanchu Y Yang Lixin L Yu Jun J Zhuang Mengru M Tang Kezhen K Shi Yuwei Y Yang Baisheng B Liu Chunqiao C Peng Bo B Ji Sheng-Jian SJ

eLife 20220218

The precise control of growth and maintenance of the retinal ganglion cell (RGC) dendrite arborization is critical for normal visual functions in mammals. However, the underlying mechanisms remain elusive. Here, we find that the N6-methyladenosine (m6A) reader YTHDF2 is highly expressed in the mouse RGCs. Conditional knockout (cKO) of Ythdf2 in the retina leads to increased RGC dendrite branching, resulting in more synapses in the inner plexiform layer. Intere ...[more]

PMID: 35179492

Similar Datasets

Quantitative proteomic analysis of mouse cerebellar granule cells after knockdown of YTHDF1

Project description:To identify the target mRNAs of YTHDF1 in granule cells, we performed quantitative proteomic analysis. Mouse cerebellar granule cells were cultured and infected with lentiviral shYthdf1 or shCtrl. Proteins were extracted. After further processing, TMT-labeled peptides were subjected to LC-MS/MS analysis. We discovered 352 proteins that were differentially expressed altogether (change fold >1.2), among which 142 proteins were downregulated after YTHDF1 KD. This study provides a protein list which shows differentially expressed proteins after knockdown of YTHDF1 in granule cells.

2022-02-15 | PXD019249 | Pride

Nitrogen source-dependent capsule induction in human pathogenic Cryptococcus species.

Project description:Cryptococcus neoformans causes meningoencephalitis and is an increasing human health threat. C. neoformans is neurotropic, and persists in the cerebrospinal fluid (CSF) of the mammalian host during infection. In order to survive in the host, pathogenic fungi must procure nutrients such as carbon and nitrogen. To enhance our understanding of nutrient acquisition during infection by Cryptococcus species, we examined utilization of nitrogen sources available in CSF. We screened for growth and capsule production of 817 global environmental and clinical isolates on various sources of nitrogen. Capsule production was assessed using ammonium and urea in the presence or absence of benomyl to determine the relationship of urea exposure to capsule production. Since urea is metabolized to ammonia and CO2 (a known signal for capsule induction), we examined urea metabolism mutants for their response to urea regarding capsule production. Non-preferred nitrogen sources were found to greatly affect capsule production in pathogenic species of Cryptococcus. Urea induced the greatest magnitude of capsule production. Capsule induction by urea was greater in Cryptococcus gattii strains than in C. neoformans strains. In addition, both environmental and clinical strains grew robustly on uric acid, casamino acids, creatinine, and asparagine as sole nitrogen sources. While substantial growth on nitrate was not apparent at day 3, growth was apparent by day 6 for all serotypes. In this study, transcription profiles of urea pathway mutants (ure1 and amt1/2) and WT Cryptococcus neoformans strains were compared in a dye-swap experiment following 1hr exposure to proline or proline + urea (.25g/L).

2013-09-25 | E-GEOD-46829 | biostudies-arrayexpress

Proteomics reveals the inhibitory mechanism of Levodopa against esophageal squamous cell carcinoma

Project description:The high recurrence rate and poor survival prospects of esophageal squamous cell carcinoma (ESCC) patients after treatment make the ongoing research on chemoprevention drugs for ESCC particularly important. In helping to solve this problem, we screened a large number of FDA-approved drugs and found that levodopa, a drug used to treat Parkinson’s disease, has an inhibitory effect on the growth of ESCC cells. To elucidate the molecular mechanisms, we applied mass spectrometry to investigate the anti-tumor activity of levodopa on ESCC. The results suggest that levodopa can down-regulate oxidative phosphorylation, non-alcoholic fatty liver disease (NAFLD) and parkinson disease pathways. SDHD, NDUFS4 and MT-CO3, major respiratory compounds in the mitochondria, were involved in these pathways. Down-regulation of these proteins is associated with mitochondrial dysfunction. Western blotting and immunofluorescence results confirmed the authenticity of proteomics data. Cell viability assay revealed that mitochondrial activity had been suppressed after levodopa treatment. Mitochondrial membrane potential reduction was detected by JC-1 and TMRE assays. And transmission electron microscope (TEM) analysis indicated that mitochondrial morphology changed. Taken together, levodopa inhibits the growth of ESCC through restraining the mitochondria.

2021-09-08 | PXD013824 | Pride

Developmental proteomics of wild-type and K6W-Ub mouse congenital cataractous lenses

Project description:Whole lenses were dissected from E15.5, P1, or P30 wild-type C57BL/6J mice or from K6W-Ub transgenic mice, which develop congenital cataracts. Lens homogenates were subjected to quantitative proteomic analysis using tandem mass tag (TMT) isobaric labeling.

2023-09-14 | PXD045040 | Pride

Ni Deprivation in Synechococcus WH8102

Project description:Two sets of microarray experiments examining the transcriptional response to Ni deprivation. One set was for growth on ammonium and the other for growth on urea Pairwise replicated comparisons (Ni deprivation in urea and ammonia)

2012-08-08 | E-GEOD-39972 | biostudies-arrayexpress

The histone variant H2A.X is a regulator of EpithelialâMesenchymal Transition

Project description:The epithelial-mesenchymal transition (EMT), considered essential for metastatic cancer, has been a focus of much research, but important questions remain. Here, we show that silencing or removing H2A.X, a histone H2A variant involved in cellular DNA repair and robust growth, induced mesenchymal-like characteristics including activation of EMT transcription factors, Slug and ZEB1, in HCT116 human colon cancer cells. Ectopic H2A.X re-expression partially reversed these changes; as did silencing Slug and ZEB1. In an experimental metastasis model, the HCT116 parental and H2A.X-null cells exhibited similar metastases levels, but the cells with re-expressed H2A.X exhibited substantially elevated levels. We surmise that H2A.X re-expression led to partial EMT reversal and increased robustness in the HCT116 cells, permitting them to both form tumors and to metastasize. In a human adenocarcinoma panel, H2A.X levels correlated inversely with Slug and ZEB1 levels. Together, these results point to H2A.X as a novel regulator of EMT. 9 samples in total including 4 replicates of control shRNA and 5 replicates of shH2A.X.

2016-02-10 | E-GEOD-75444 | biostudies-arrayexpress

A high protein model alters the endometrial transcriptome of mares

Project description:We developed an experimental model to elevate BUN during diestrus. There were both urea and control treatments (7 mares/treatment), done in a crossover design. Urea treatment consisted of a loading dose of urea (0.03 g/kg of urea) and urea injections over 6 hours (0.03 g/kg/hr). Control mares received the same volume of saline solution. Blood samples were collected to measure BUN. Uterine and vaginal pH were evaluated after the last intravenous infusion, then endometrial biopsies were collected for RNA-sequencing

2019-09-18 | GSE131810 | GEO

Haploid and diploid Emiliania huxleyi (RCC 1217 and RCC1216) under P starvation

Project description:Haploid (1N) and diploid (2N) Emiliania huxley (RCC 1217 and RCC1216) were grown in dilute batch culture and achieved stationary phase. We sampled two time points, at early (T2) and late (T3) stationary phase. Controls are haploid or diploid cells derived from dilute cultures (T1) growing in replete control medium. All samples were hybridized against a common, pooled baseline RNA. All experiments and hybridization were done in independent biological triplicates (A, B and C).

2016-03-29 | E-MTAB-3877 | biostudies-arrayexpress

urea-Urea impact on the nitrogen metabolism of plant and on the nitrogen transport systems

Project description:ra05-09_urea - urea - What are the transcriptomic plant responses to urea nitrogen supply ? - Columbia Arabidopsis ecotype were grown hydroponically on 0.5 mM NH4NO3 as sole nitrogen source during 35 days under short days. Plants were then placed on 3 nutrient solutions supplemented, either with 1 mM NH4NO3, or with 0.5 mM NH4NO3 + 0.5 mM Urea, or with 1 mM Urea. Root and shoot samples were harvested separately 7 days after these different nitrogen treatments Keywords: treated vs untreated comparison

2007-10-16 | GSE9258 | GEO

Evaluation of the Effect of Trypsin Digestion Buffers on Artificial Deamidation

Project description:This work comprehensively compared 50 mM of ammonium acetate (pH 6), Tris-HCl (pH 8), ABC and TEAB as in-solution trypsin digestion buffers. Both iTRAQ quantification and label-free results indicate that ammonium acetate (pH 6) is more suitable than other buffers for studying endogenous deamidation and N-glycosylation due to the significant decrease of artificial Asn deamidation in comparison to other buffers without affecting protein and peptide identification and Gln deamidation. Determination of the half-life of Asn deamidation in the four buffers further validates the conclusion. Our results also indicate that among the commonly used tryspin digestion buffers, ABC and TEAB are not suitable for studying Asn deamidation and N-glycosylation, but Tris-HCl may be used if trypsin digestion has to be done at around pH 8.

2022-02-28 | PXD001650 | Pride