Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Application of the HCC spectral library in DIA quantitation

ABSTRACT: This project stores the search results of MaxQuant2.0.3.0 of 162 HCC cell line raw files and 48 raw files for spectral library generation, and search results of DIA-NN version 1.8 and Spectronaut version15.2 of HepG2, HCCLM3 and TGFB1-stimulated HCCLM3.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Liver

SUBMITTER: Mingchao Wang

LAB HEAD: Wang mingchao

PROVIDER: PXD037159 | Pride | 2022-11-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Control_R1.raw	Raw
	Control_R2.raw	Raw
	Control_R3.raw	Raw
	EMT_R1.raw	Raw
	EMT_R2.raw	Raw

Items per page:

1 - 5 of 25

Similar Datasets

Generation of the HCC spectral library covering more than 10,000 protein groups

Project description:Peptides of HCC cell lines and tumour tissues were fractionated by Hp-RP to eight fractions and repeated analysed three times by the LC-MS/MS detection system consisted of the EASY-nLC 1000 coupled to the Q-Exactive HF mass spectrometer using data dependent acquisition mode.

2022-11-11 | PXD035028 | Pride

Proteome of Human hepatocellular carcinoma cell lines

Project description:The proteomic profiling of nine commonly used HCC cell lines Hep3B, HepG2, HepG2.2.15, HUH7, PLC/PRF/5, MHCC97L,MHCC97H,HCCLM3 and HCCLM6

2022-11-11 | PXD036643 | Pride

The impact of codon usage from bicistronic mRNA on their transcriptomic, post-transcriptomic and proteomic regulation in human cells

Project description:A large amount of virus infecting humans expresses polycistronic mRNAs on which viral ORF display codon usages (CU) dissimilar to the average human ORF CU. Among those viruses, oncogenic Human Papillomavirus (HPV) are responsible for 5% of all cancer cases. It is known that CU is a major step of both quantitative and qualitative translation regulation. On top of that, human translation machinery mainly come across monocistronic mRNAs. The translation of downstream ORF on polycistronic mRNAs is generally ill-defined, relying on non-canonical translation mechanisms. CU variation could also modulate downstream ORF translation. We believe that poorly matching CU between polycistronic viral mRNAs and the translation machinery of its host may have conferred oncogenic HPVs an evolutionary advantage by reducing viral protein expression, facilitating immune escape, persistence of infection and establishment of carcinogenesis. To unravel variables influencing viral mRNAs regulation, we expressed in the U-2 OS cell line 13 versions of an shble_gfp bicistronic mRNA which i) mimic the e6_e7 mRNA from HPVs, ii) display 13 different CU to code the same SHBLE protein and, iii) for 5 version undergo splicing in shble ORF (which was latter castrated given us a total of 18 constructs). We then quantified, mRNA expression, splicing efficiency, GFP fluorescence and, SHBLE and GFP expression via mass-spec. We first confirmed that monocistronic gfp mRNAs are a 100 times more efficiently translated than any shble_gfp bicistronic mRNAs. No impact was found of shble CU on mRNA transcription levels. The 5 versions comparison between spliced vs. mutated revealed a positive impact of shble splicing on GFP translation. Next, we showed that CU greatly affect the expression of SHBLE. Finally, we strikingly showed that the variation in CU and SHBLE expression does not significantly affect downstream GFP expression, suggesting that GFP is translated via leaky scanning.

2025-05-06 | PXD047576 | Pride

Time-course expression QTL atlas of the global transcriptional response of wheat to Fusarium graminearum

Project description:We have captured transcriptomes of 196 doubled haploid wheat lines segregating for Fusarium head blight resistance after inoculation with the pathogen Fusarium graminearum at 30 and 50 hours after inoculation. The pathogen switches from biotrophic to nectrotrophic lifestyle in course of disease development forcing its host to adapt its defence strategies. We performed an eQTL analysis on both time points and describe the changing segregating response to the pathogen in time. Our analysis describes three major regulatory hotspots that govern the expression of 1000s of genes and eQTL colocalizing with phenotypic resistance QTL.

2016-11-16 | E-MTAB-5127 | biostudies-arrayexpress

Transcription profiling of 20 human primary high grade glioma cell cultures

Project description:Gene expression profiling of 20 primary high grade glioma cell cultures

2007-05-31 | E-MEXP-1063 | biostudies-arrayexpress

LncRNA/mRNA expression profiling for THP-1 macrophages and THP-1 macrophage-derived foam cells

Project description:By identifying differentially expressed LncRNAs/mRNAs in THP-1 macrophages and THP-1 macrophage-derived foam cells, we select some differentially expressed LncRNAs and explore their roles in atherosclerosis process. We already find that some LncRNA can effect cholesterol metabolism and level of inflammation factor, which may influence atherosclerosis process. In the study presented here, 6 human samples were used to acquire expression profiles, which provide futher insight into the pathologies of atherosclerosis

2014-05-20 | E-GEOD-54039 | biostudies-arrayexpress

miRNA chronic OVA aerosol

Project description:specific pathogen-free female BALB/c mice aged 7-8 weeks (Animal Resources Centre, Perth, Western Australia) were systemically sensitised by intraperitoneal injection of 50 M-5g of alum-precipitated chicken egg OVA (Grade V, ?98% pure, Sigma Australia) 21 and 7 days before inhalational challenge, then exposed to aerosolised OVA in a whole body inhalation exposure chamber (Unifab Corporation, Kalamazoo, MI). Chronic low-level challenge involved exposure to ?3 mg/m3 aerosolised OVA for 30 minutes/day on 3 days/week for up to 6 weeks. Particle concentration within the chamber was continuously monitored using a DustTrak 8520 instrument (TSI, St Paul, MN). All experimental procedures complied with the requirements of the Animal Care and Ethics Committee of the University of New South Wales (reference numbers: 06/119B and 08/09B). Mice were sacrificed after 1,2,4 and 6 weeks of OVA exposure. Control groups included naM-ove mice and mice that were not sensitised but were challenged for 6 weeks with aerosolised OVA.

2011-06-10 | E-MEXP-3118 | biostudies-arrayexpress

Transcription profiling of C3H/HeJ and JF1/Msf strain mice to identify genetic risk factors for asthma and COPD

Project description:Comparison of lung function in C3H/HeJ and JF1/Msf strain mice to identify genetic risk factors for asthma and COPD.

2007-03-08 | E-MEXP-855 | biostudies-arrayexpress

Transcription profiling of wild type and Ahr(-/-) mouse embryo fibroblast cells

Project description:Wildtype vs. Ahr(-/-) mouse embryo fibroblast cells were compared in a flipped-dye design

2006-10-17 | E-MEXP-787 | biostudies-arrayexpress

Transcription profiling of mouse T cell sub-populations isolated from pulmonary tissue after mice were exposured to filtered air of acrolein for one week

Project description:Mice were exposed to filtered air or acrolein for 1 week. T cell subpopulations were isolated from the pulmonary tissue by cell sorting.

2008-11-15 | E-MEXP-1354 | 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