Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human hepatocellular carcinoma MHCC97H proteome

ABSTRACT: In this work, we generated a MHCC97H proteome datasets by In-gel digestion on Orbitrap Fusion Lumos. We systematically compared RNC-seq and Ribo-seq in the context of proteome identification, especially when identifying protein isoforms from AS. We also demonstrated that the single-molecule long read sequencing technique identified thousands of new splice variants and guided the MS identifications of new protein isoforms.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hepatocyte, Cell Culture

SUBMITTER: wang hongwei

LAB HEAD: Gong Zhang

PROVIDER: PXD032201 | Pride | 2022-06-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Efficient Detection of the Alternative Spliced Human Proteome Using Translatome Sequencing.

Wu Chun C Lu Xiaolong X Lu Shaohua S Wang Hongwei H Li Dehua D Zhao Jing J Jin Jingjie J Sun Zhenghua Z He Qing-Yu QY Chen Yang Y Zhang Gong G

Frontiers in molecular biosciences 20220602

Alternative splicing (AS) isoforms create numerous proteoforms, expanding the complexity of the genome. Highly similar sequences, incomplete reference databases and the insufficient sequence coverage of mass spectrometry limit the identification of AS proteoforms. Here, we demonstrated full-length translating mRNAs (ribosome nascent-chain complex-bound mRNAs, RNC-mRNAs) sequencing (RNC-seq) strategy to sequence the entire translating mRNA using next-generation sequencing, including short-read an ...[more]

PMID: 35720116

Similar Datasets

Expression analysis of effect of Intestine-specific knockdown of KLF5 on radiation induced intestinal injury

Project description:The objective was to determine the role of Krüppel-like factor 5 (KLF5) in radiation-induced intestinal injury. Mice with intestinal-specific knockdown of KLF5 (Cre+ mice) were generated and their response to radiation was compared with controls (Cre- mice). Mice were given 15 Gy total body irradiation (TBI). The mice intestines were harvested at 6h post TBI and screened for differentially expressed genes by microarray analysis. We identified 11,004 and 2,466 differentially expressed genes in non-irradiated and irradiated mice at 6h post TBI, respectively. KLF5 knockdown down-regulated genes related to DNA damage repair pathways such as nucleotide excision repair, mismatch repair, non-homologous end joining and the Fanconi anemia pathway, which may suggest a novel function of KLF5. A four chip study using total RNA recovered from four pooled intestine tissues of four experimental groups. The four experimental groups respectively were the 6h-cre+ group, 6h-cre- group, con-cre+ group and con-cre- group. Equal mass amounts of total RNA were pooled from each small intestine to yield a sample representing RNA from 3 separate mice in each group. One pooled sample in every group were tested with one chip. Each chip measures the expression level of 44,170 genes from C57BL/6 mouse (background) with three 60-mer probe pairs per gene.

2015-03-10 | E-GEOD-66655 | biostudies-arrayexpress

Transcriptome and DNA (hydro)methylation in mouse hypothalamic arcuate nucleus in puberty onset.

Project description:To better understand the epigenetic mechanism underlying pubertal onset, the hypothalamic genome-wide DNA methylation and hydroxymethylation patterns as well as the transcription profiles in mouse arcuate nucleus at early and late pubertal stages were explored. Female mice have been widely used in multiple studies on pubertal development as they present the similar molecular behaviors in HPG axis and stable cycles of menstrual calendar like human. Hypothalamic ARC underwent a huge epigenetic and genetic reprogramming to adapt to the response and feedback on sexual hormones during the stages of early pubertal (2-5-week of age) and late puberty (5-8-week of age) . We harvested 4- and 8-week hypothalamic ARC and employed RNA-seq, reduced representation bisulfite sequencing (RRBS) and hydroxymethylation profiling (RRHP) on a genome-wide scale. We identified a large number of differential expressed genes (DEGs) and differential 5(h)mC signals across the whole genome. We discovered novel connections between DNA (hydroxyl)methylated modification and gene expression, emphasizing the importance of epigenetic alterations in regulating transcription in puberty onset.

2020-08-20 | E-MTAB-9420 | biostudies-arrayexpress

XRN2 Autoregulation and Control of Polycistronic Gene Expression in Caenorhabditis elegans

Project description:XRN2 is a conserved 5â??-->3â?? exoribonuclease that complexes with XTB-domain containing proteins. Thus, in Caenorhabditis elegans (C. elegans), the XTBD-protein PAXT-1 stabilizes XRN2 to retain its activity. XRN2 activity is also promoted by 3'(2'),5'-bisphosphate nucleotidase 1 (BPNT1) through its hydrolysis of 3â??-phosphoadenosine-5'-bisphosphate (PAP), an endogenous XRN inhibitor. Here, we find through unbiased screening that loss of bpnt-1 function suppresses lethality caused by paxt-1 deletion. This unexpected finding is explained by XRN2 autoregulation, which occurs through repression of a cryptic promoter activity and destabilization of the xrn-2 transcript. Autoregulation appears to be triggered at different thresholds of XRN2 inactivation, such that more robust XRN2 perturbation, by elimination of both PAXT-1 and BPNT1, is less detrimental to worm viability than absence of PAXT-1 alone. Like more than 15% of C. elegans genes, xrn-2 occurs in an operon, and we identify additional operons under its control, consistent with a broader function of XRN2 in polycistronic gene regulation. Regulation occurs through intercistronic regions that link genes in an operon, but similar mechanisms may allow XRN2 to operate on monocistronic genes in organisms lacking operons. Wild-type C. elegans worms were subjected to mock or xrn-2 RNAi from L1 to L4 stage at 20Â°C. Total RNA was extracted from the worms, and polyadenylated RNA was analyzed.

2016-08-25 | E-GEOD-79994 | biostudies-arrayexpress

RNA expression profiling in primary and immortalized human mesothelial cells, and in human vein and microvascular endothelial cells

Project description:Mesothelial cells, which interact with endothelial cells, are widely used in research including cancer and drug development, have not been comprehensively profiled. We therefore performed RNA sequencing of polarized, primary peritoneal (HPMC) and immortalized pleural mesothelial cells (MeT-5A), and compared it to endothelial cells from umbilical vein (HUVEC) and cardiac capillaries (HCMEC).

2023-05-24 | E-MTAB-12021 | biostudies-arrayexpress

Genome-wide occupancy of H3K27me3 in human gingival mesenchymal and periodontal ligament stem cells in response to Electronic-cigarette

Project description:The epigenetic regulation on gene transcription affected by Electronic-cigarette (E-cig) to human gingival mesenchymal (GMSC) is not fully understood. Here, we collected GMSCs from systemically healthy patients due to the premolars and extracted for orthodontic reasons, and treated with E-cig smoke with original flavor (G2), E-cig smoke with menthol flavor (G3), E-cig liquid with original flavor (G4), and E-cig liquid with menthol flavor (G5) by the optimal conditions of LC50, and conducted H3K27me3 ChIP-seq to compare with untreated control (G0).

2022-09-03 | E-MTAB-12079 | biostudies-arrayexpress

IL-2Rα-biased, but not βγ-biased, agonist reprograms tumor immune landscape and synergize with αPD-1 therapy

Project description:We investigated whether exogenous supplies of different IL-2R agonists (IL-2wt, IL-2nα or IL-2α-bias) at the concentration of 3 mg/g body weight could rescue the transcriptional signatures of dysfunctional T cells in large tumors, or allow them to regain sensitivity to αPD-1 antibody. Remarkably, after transient stimulation by IL-2wt, large tumors fully restored the effector/activation signatures observed in small tumors, such as upregulation of effector genes (Gzma, Gzmb, Gzmk and Ifng), T cell activation/exhaustion genes (Ctla4, Pdcd1, Lag3 and Havcr2), inflammatory cytokine/cytokine receptors (Il2ra, Il2rb, Il2rg and Il21r), and chemokines (Cxcl9, Cxcl10 and Ccl19) (Fig.7d). Surprisingly, although IL-2α-bias had >10-fold weaker in vitro activity than IL-2wt, and could only activate the small fraction of CD25-upregulated CD8+Teff cells, the transcriptional profiles were indistinguishable between IL-2wt and IL-2α-bias treated large tumors. In stark contrast, IL-2nα treatment showed no meaningful transcriptional changes in large tumors compared to untreated control. These results once again demonstrate the critical role of CD25 in transmitting IL-2 signaling to reprogram the tumor immune microenvironment.

2023-04-02 | E-MTAB-12372 | biostudies-arrayexpress

Comprehensive Landscape of SA-AKI Revealed by Integrated Proteomics and Metabolomics Analysis

Project description:Sepsis-associated acute kidney injury (SA-AKI) is a severe and life-threatening condi-tion with high morbidity and mortality among emergency patients, and it poses a sig-nificant risk of chronic renal failure. Clinical treatments for SA-AKI remain reactive and non-specific, lacking effective diagnostic biomarkers or treatment targets. In this study, we established an SA-AKI mouse model using LPS and performed proteomics and metabolomics analyses. A variety of bioinformatic analyses, including Gene Set En-richment Analysis (GSEA), Weighted Gene Co-expression Network Analysis (WGCNA), protein and protein interactions (PPI), and MetaboAnalyst analysis, were conducted to investigate the key molecules of SA-AKI. Proteomics and metabolomics analyses re-vealed that sepsis led to impaired renal mitochondrial function and metabolic disorders. Immune-related pathways were found to be activated in kidneys upon septic infection. The catabolic products of polyamines accumulated in septic kidneys. Overall, our study provides a more comprehensive understanding of SA-AKI and identifies potential pathways for this condition.

2023-10-24 | PXD044371 | Pride

The comparison of exosomal miRNAs from ECM or media derived from HFF-CBD-Lamp2b cells, HFF cells, HFF-Lamp2b cells and hUCMSCs

Project description:The next-generation sequencing technology was used to investigate the difference of RNAs content among the different types of exosomes from the media of HFF cells, HFF-Lamp2b cells and hUCMSCs, and from the ECM of HFF-CBD-Lamp2b cells

2021-10-12 | E-MTAB-10905 | biostudies-arrayexpress

Sus scrofa, skeletal muscle, LC-MSMS

Project description:Skeletal muscle were collected from pigs treated in the control group, the Lys deficiency group and the Lys rescue group. Then, the samples were analyzed by LC-MSMS.

2020-05-27 | PXD016396 | Pride

RNA and cell free miRNA in one family of Kallmann's syndrome

Project description:Kallmann Syndrome (KS) is a rare human genetic disorder characterized by the hypogonadotropic hypogonadism with the reduction or absence of olfactory sense. The mutations on the multiple genes including Chemokine Prokineticin-2 (PROK2) were considered to contribute to the abnormal migration of gonadotropin-releasing hormone (GnRH) neurons in embryonic stage. Here, we submit RNA-seq of the peripheral blood and the cell free miRNA-seq in the serum of one family, in which the KS patient has the same mutation of PROK2 (c.223-4C>A) with his mother, and the genetic phenotype of his father is normal. The sexual development and function of his parents are normal.

2020-05-01 | E-MTAB-8919 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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