Analysis of transcriptome changes of human epidermal stem cells treated by EGF
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ABSTRACT:
PROVIDER: PRJNA656761 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12435924_1.fastq.gz | Fastqsanger.gz | |||
| SRR12435924_2.fastq.gz | Fastqsanger.gz | |||
| SRR12435925_1.fastq.gz | Fastqsanger.gz | |||
| SRR12435925_2.fastq.gz | Fastqsanger.gz | |||
| SRR12435926_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the application of transcriptome sequencing technology in the analysis of transcriptome changes in human epidermal stem cells after EGF incubation. We found that EGF can significantly change the gene transcription of human epidermal stem cells. There are 3,759 differential genes, which are highly related to wound healing and the proliferation and differentiation of epidermal stem cells. This study provides a basis for comprehensive analysis of the effect of EGF/EGFR pathway on epidermal stem cells.
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Project description:Primary cultures of astrocytes from rat optic nerve heads were treated with EGFR ligand, EGF. Two cell lines from two different rat donors were used. The sister cell cultures were set as control and EGF treated groups. Experiment Overall Design: experiment #1: compared control astrocyte cultures to sister cultures treated with EGF for 4 hours. Experiment Overall Design: experiment #2: compared control astrocyte cultures to sister cultures treated with EGF for 12 hours
2007-11-29 | E-GEOD-5282 | biostudies-arrayexpress
Project description:GBM neurosphere line GBM1B were depleted of growth factors for 16 hours followed by EGF stimulation for 4 and 24 hours. RNA-seq was used to identify differentially-expressed (DE) genes after EGF treatment.
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Project description:Normal human epidermal keratinocytes (NHEK) from neonatal foreskin were cultured in serum-free EpiLife medium with human KC growth supplement (0.2% bovine pituitary extract (v/v), 5ug bovine insulin, 5ug/ml bovine transferrin, 0.5ng/ml human EGF, and 0.18 ug/ml hydrocortisone) from Cascade Biologics. Cultures were treated with recombinant cytokines from R&D Systems. J Immunol. 2007 Feb 15;178(4):2229-40. Keywords: cytokine response
2007-03-09 | GSE7216 | GEO
Project description:Transcriptome profiling by using RNA-seq was performed on bleogen pB1-treated, EGF-treated, and untreated HaCaT keratinocytes to gain further insights into the wound healing effects of bleogen pB1 and EGF
2022-09-15 | GSE202512 | GEO
Project description:Epidermal growth factor (EGF) is a potent mitogenic agent promoting cell differentiation, proliferation, and growth. The kidney thick ascending limb of Henle’s loop and distal convoluted tubule were identified as major sites of EGF synthesis. As expected, EGF can modulate the functioning of kidney collecting duct including osmotic water permeability (Pf). Here, we found that EGF (0.1 uM) reduced the vasopressin-stimulated Pf by 26% in isolated perfused rat inner medullary collecting duct (IMCD). Immunoblotting using IMCD suspensions prepared in similar condition showed that EGF significantly reduced phosphorylation of AQP2 at Ser264 and Ser269 but had not affected on Ser256 or proline-directed Ser261 site. Quantitative phosphoproteomics was carried out to investigate other effects of EGF. Rat IMCD suspensions were treated with 1 M of EGF or vehicle for 30 min. Samples from three replicates of experiment were analyzed by TMT isobaric labeling quantitative protein mass spectrometry. We identified 23859 phosphopeptides with unique phosphorylation sites in EGF-treated rat IMCD samples, with 25 proteins increased and 100 proteins decreased in phosphorylation as determined by dual statistical analysis. EGF induced phosphorylation of multiple residues at the C-terminus of EGF receptor, EGFR or Erbb1, and mildly activated the classical MAPK pathway, RAF-MEK-ERK. EGF also affected phosphorylation of several proteins in PI3K/Akt pathway involved in cap-dependent translation initiation (Eif4ebp1, Gigyf2, Eif3b, Eif4g3, Pdcd4) and translation elongation (Eef2k, Eef2), predicted an overall translation repression. In comparison with a dDAVP-induced phosphoproteome, we found that the majority of proteins had phosphorylation change on specific site by either EGF or dDAVP but not both, suggesting a highly selectivity of phosphorylation modification induced by these two agents. Among the 25 peptides that had phosphorylation change on the same site by both EGF and dDAVP, AQP2 at Ser264/Ser269 was changed in opposite direction. We concluded that the short-term effect of EGF is insufficient to cause an effect on Ser261 phosphorylation of AQP2 in normal rat IMCD.
2025-06-26 | PXD017192 | Pride
Project description:Translatome analysis by sucrose gradient centrifugation of cell lysates followed by microarray profiling of the polysomal and subpolysomal RNA fractions represents a way of both studying translational control networks and better approximating the proteomic representation of cells. It is an established notion that translational control takes place essentially at the translation initiation level, therefore the variation in abundance of a given mRNA species on polysomes can be directly related to the variation in abundance of the corresponding protein. Comparison of translatome profile changes with corresponding transcriptome profile changes can provide a measure of the degree of concordance between cellular controls affecting mRNA abundance and cellular controls affecting mRNA availability to translation. To provide a direct experimental evaluation of the phenomenon, we decided to study a classical example of transcriptional reprogramming of gene expression: Epidermal Growth Factor (EGF) treatment. This stimulus triggers a well known chain of intracellular transduction events, ultimately resulting in a multifaceted phenotypic spectrum of changes with prevalent induction of cell growth and proliferation. We subjected HeLa cells to serum starvation for 12h and then we added EGF at final concentration of 1 μg/ml, profiling before and after 40 minutes of treatment the transcriptome, the translatome, coming from the polysomal pool of mRNAs after sucrose gradient separation, and also the mRNA content of the subpolysomal pool, expected not to be actively translated. Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, EGF starvation release. The comparison between transcriptional and polysomal profiling was used for the discovery of general and mRNA-specific changes in the translation state of the serum starved HeLa cells transcriptome in response to EGF stimulus. To identify translationally regulated mRNA molecules, gene expression signals derived from the polysomal and subpolysomal RNA populations were compared by microarrays analysis to those obtained from unfractionated total RNAs. Polysomal RNA, subpolysomal RNA and total RNA were isolated from HeLa cells serum starved and treated with EGF. Cells lysates were collected before (t = 0 min) and after (t = 40 min) EGF treatment. All experiments were run in triplicates.
2010-05-27 | E-GEOD-20277 | biostudies-arrayexpress
Project description:Hematopoietic aging is associated with decreased hematopoietic stem cell (HSC) self-renewal capacity and increased risk for myelodysplasia and leukemia. Deficient DNA repair contributes to the decline in HSC self-renewal capacity during aging and it remains unclear whether extrinsic signals can rejuvenate aged HSCs. Here, we demonstrate that augmentation of non-homologous end-joining (NHEJ) DNA repair in aged HSCs via treatment with epidermal growth factor (EGF) rejuvenates HSC function. Seven day culture of BM CD34-ckit+sca-1+lin- (34-KSL) HSCs from aged C57BL/6 mice with EGF suppressed myeloid skewing and increased production of multipotent CFU-granulocyte, erythroid, monocyte and megakaryocyte (CFU-GEMM) colonies. Aged, EGF-treated HSCs displayed increased donor multilineage engraftment in primary competitively transplanted mice and in secondary mice compared to mice transplanted with aged, control HSCs. Donor cell engraftment within the bone marrow (BM) KSL and SLAM+KSL HSC population was > 2-fold increased in mice transplanted with aged, EGF-treated HSCs. Systemic administration of EGF to aged mice for 6 weeks also increased long term – HSC self-renewal capacity as measured by increased donor bone marrow (BM) competitive repopulation in primary and secondary transplanted mice. Conversely, deletion of EGFR in Scl/Tal1+ hematopoietic cells was associated with increased myeloid skewing and depletion of LT-HSCs in middle aged mice. Mechanistically, EGF treatment decreased DNA damage in aged HSCs through activation of DNA PK-cs, Artemis and NHEJ repair. Inhibition of DNA PK-cs blocked EGF-mediated restoration of multipotent differentiation and suppression of myeloid skewing in aged HSCs, suggesting that the restoration of hematopoietic potential in aged HSCs is dependent on EGF-mediated activation of DNA PK-cs. EGF treatment also converted the transcriptome of aged HSCs from enrichment for genes involved in cell death and survival to genes involved in HSC generation and identity. These data suggest that extrinsic activation of EGFR signaling can restore key functional capacities in aged HSCs.
2024-04-01 | GSE252293 | GEO