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MRNA and RNC-mRNA deep sequencing of three hepatocellular carcinoma cell lines

ABSTRACT: We sequenced the total mRNA and translating mRNA (RNC-mRNA) of three hepatocellular carcinoma cell lines Hep3B, HCCLM3 and MHCC97H

ORGANISM(S): Homo sapiens

PROVIDER: GSE49994 | GEO | 2014/02/18

SECONDARY ACCESSION(S): PRJNA215765

REPOSITORIES: GEO

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mRNA and RNC-mRNA deep sequencing of three hepatocellular carcinoma cell lines

Project description:We sequenced the total mRNA and translating mRNA (RNC-mRNA) of three hepatocellular carcinoma cell lines Hep3B, HCCLM3 and MHCC97H For each cell line, samples prepared from three independent and identical cell cultures were pooled with equal amounts. C-HPP China Team

2014-02-18 | E-GEOD-49994 | biostudies-arrayexpress

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

LncRNA regulated by hnRNPAB in HCC cell lines

Project description:To reveal the HNRNPAB-regulated lncRNAs, we performed microarray analyses to screen differential lncRNAs in HCC cells after stable overexpression or knockdown of HNRNPAB. MHCC97H and HCCLM3 (HCC cell lines with high-metastatic potentials), PLC/PRF/5 and HepG2 (HCC cell lines with low-metastatic potentials) were used in this study. HepG2-control, HepG2-hnRNPAB, PLC/PRF/5-control, PLC/PRF/5-hnRNPAB, MHCC97H-control, MHCC97H-sh-hnRNPAB, HCCLM3-control, HCCLM3-sh-hnRNPAB were perpared with hU6-MCS-CBh-gcGFP-IRES-puromycin-shRNA-HNRNPAB/mock lentiviral and Ubi-MCS-SV40-EGFP-IRES-puromycin-HNRNPAB/mock cDNA lentiviral,respectively, each performed in triplicate.

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Project description:It is known that exosomes (endosome derived vesicles) play important roles in the formation of the tumor microenvironment. Hepatocellular carcinoma (HCC) is a highly malignant cancer, whose malignancy is largely influenced by the tumor microenvironment. The possible role and the specific content of the HCC derived exosomes are however largely unknown. We performed super-SILAC-based mass spectrometry (MS) analyses to interrogate the differential proteins in the exosome of three human HCC cell lines, MHCC97H, MHCCLM3 and Hep3B cells. Exosomal proteins were systematically compared with multi-omics strategies, considering both proteomics and translatomics. With stringent data quality control (quantified unique peptides ≥ 2, FDR ≤ 0.01 at both protein and peptide level), 1907 exosomal proteins were confidently identified from the three HCC cell lines, out of which 469 and 443 exosomal proteins significantly altered in the highly malignant cell lines (MHCC97H/Hep3B and MHCCLM3/Hep3B), respectively. ClueGo and IPA analyses on the differentially expressed proteins (DEPs) revealed that translation and ubiquitination biological processes pathways were significantly more encapsulated in the exosome of higher malignant cell lines. We further observed significantly negative correlation of exosomal protein to cellular protein and translating mRNA in terms of relative abundances comparing the higher malignant cell lines with the low malignant cell line. The negatively correlated genes are also translation regulation-centric. In conclusion, we demonstrated that the exosomal enrichment of translation regulatory proteins is related to the malignant level of HCC cells.

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Transcriptome analysis of the C. glutamicum deletion mutant of rnc, which encodes an RNase III homolog

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Project description:We compared standard human reference genome GRCh38 and de novo assembled reference genome HX1 in precision medicine applications for specific ethnics. In order to quantify the HX1 misassembled genes and HX1-specific contigs, we performed RNA-seq and RNC-seq on hepatocellular carcinoma cell lines (MHCC97H, MHCCLM3 and MHCCLM6) which were derived from Chinese Han individuals. In which, RNC-seq datasets of MHCC97H and MHCCLM3 had been published. We found that a considerable fraction of HX1 misassembled genes was expressed in the Chinese Han samples. Furthermore, we found no HX1-specific contigs yielded more than 2.27 FPKM (minimun FPKM of 1 copy/cell transcript) in the Chinese Han sampels.

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RNA-seq and RNC-seq of S1K247Q, S1K247R, and S1WT

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Transcription profiling by array of Staphylococcus aureus wild type and rnc, pnp and sigB mutants

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Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells

Project description:In the process of translation, ribosomes first bind to mRNAs (translation initiation) and then move along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. By employing three types of RNA-seq methods, we experimentally and computationally resolved elongation speed at individual gene level and under physiological condition in human cells. We proposed the elongation velocity index (EVI) as a relative measure and successfully distinguished slow-translating genes from the background translatome. The proteins encoded by the low-EVI genes are more stable than the proteome background. In normal cell and lung cancer cell comparisons, we found that the relatively slow-translating genes are relevant to the maintenance of malignant phenotypes. In addition, we identified cell-specific slow-translating codons, which may serve as a causal factor of elongation deceleration. We sequenced mRNA, translating mRNA (RNC-mRNA) and ribosome footprints in normally growing HeLa cells.

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