Dataset Information

Proteomics of human lens epithelial cells under normoxia and hypoxia

ABSTRACT: The HLE cells were seeded in three 10cm Petri dishes overnight and treated for 24h under hypoxia(1% O2) and normoxia conditions respectively. The treated cells were collected as samples, and subjected to Tandem Mass Tag (TMT) Labeling and High pH Reversed-Phase Peptide Fractionation.

ORGANISM(S): Homo Sapiens

SUBMITTER: Xingchao Shentu

PROVIDER: PXD041436 | iProX | Mon Apr 10 00:00:00 BST 2023

REPOSITORIES: iProX

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Publications

Glycolysis Aids in Human Lens Epithelial Cells' Adaptation to Hypoxia.

Huang Yuxin Y Ping Xiyuan X Cui Yilei Y Yang Hao H Bao Jing J Yin Qichuan Q Ailifeire Hailaiti H Shentu Xingchao X

Antioxidants (Basel, Switzerland) 20230619 6

Hypoxic environments are known to trigger pathological damage in multiple cellular subtypes. Interestingly, the lens is a naturally hypoxic tissue, with glycolysis serving as its main source of energy. Hypoxia is essential for maintaining the long-term transparency of the lens in addition to avoiding nuclear cataracts. Herein, we explore the complex mechanisms by which lens epithelial cells adapt to hypoxic conditions while maintaining their normal growth and metabolic activity. Our data show th ...[more]

PMID: 37372033

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Project description:Purpose: The goal of this study is to identify the mRNA clusters that are regulated by EGFR under normoxia or hypoxia. Method: Total RNAs were extracted from HeLa cells expressing scrambled control or EGFR shRNA-E1 that cultured under normoxia or hypoxia (1% O2) for 24h. Customized Next-Generation RNA Deep Sequencing, including both small RNA application and whole transcriptome analysis, was performed according to the standard procedure instructed by Applied Biosystems. For whole transcriptome analysis, SOLiD fragment colorspace transcriptome reads (50nt) were mapped to the human genome (hg19) and assigned to ensemble transcripts using Bioscope 1.3.1 (Life Technologies). The values of reads per kilobase per million reads (RPKM) were determined by Bioscope 1.3.1 CountTags tool using default parameters. Primary alignments with a minimum mapping quality of 10 and minimum alignment score of 10 were counted. Results: Deep sequencing analysis identified subclasses of mRNAs that were affected by EGFR either under normoxia or hypoxia. EGFR-regulated mRNAs (with Log2 fold-change affected by EGFR M-bM-^IM-% 0.4 or M-bM-^IM-$ -0.4) were sorted and over-lapped with mRNAs that were targeted (based on published data and TargetScan prediction with total context score M-bM-^IM-$ -0.20) by the top miRNA candidates affected by EGFR under hypoxia, resulting in 439 mRNAs that regulated by EGFR and likely targeted by the miRNA candidates in response to hypoxia. Conclusion: Whole transcriptome analysis revealed a novel cluster of mRNAs that are likely regulated by EGFR through miRNAs in response to hypoxic stress. RNA profiles of HeLa cells expressing scrambled control (S) or EGFR shRNA-E1 (A1) that cultured under normoxia or hypoxia (1% O2) for 24h were generated by AB SOLiD curstomarized next-generation sequencing, including both small RNA application and whole transcriptome analysis. S: HeLa expressing scrambled control cultured under normoxia; A1: HeLa expressing EGFR shRNA-E1 cultured under normoxia; HS: HeLa expressing scrambled control cultured under hypoxia for 24h; HA1: HeLa expressing EGFR shRNA-E1 cultured under hypoxia for 24h. In total, 4 biological samples with no replicates resulted in 4 whole transcriptome RNA profiles.

Dataset Information

Proteomics of human lens epithelial cells under normoxia and hypoxia

Publications

Glycolysis Aids in Human Lens Epithelial Cells' Adaptation to Hypoxia.

Similar Datasets

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