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Unknown,Transcriptomics,Genomics,Proteomics

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RNA seq of epidermal tissue after acute repetitive irradiation

ABSTRACT: Whole transcriptome sequencing data generated from epidermal samples (suction blister roofs) of healthy female subjects after repetitive irradiation on three consecutive days using a full spectrum solar simulator. RNA was extracted from suction blisters taken from irradiated and control sites on the lower backs of each subject 24 hours after the final irradiation. RNA was cDNA converted and then sequenced on an Illumina HiSeq 2500 (single-end, 50 bp) to an approximate sequencing depth of 100 million reads per sample.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Nicholas Holzscheck

PROVIDER: E-MTAB-9251 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Concomitant DNA methylation and transcriptome signatures define epidermal responses to acute solar UV radiation.

Holzscheck Nicholas N Söhle Jörn J Schläger Torsten T Falckenhayn Cassandra C Grönniger Elke E Kolbe Ludger L Wenck Horst H Terstegen Lara L Kaderali Lars L Winnefeld Marc M Gorges Katharina K

Scientific reports 20200731 1

The simultaneous analysis of different regulatory levels of biological phenomena by means of multi-omics data integration has proven an invaluable tool in modern precision medicine, yet many processes ultimately paving the way towards disease manifestation remain elusive and have not been studied in this regard. Here we investigated the early molecular events following repetitive UV irradiation of in vivo healthy human skin in depth on transcriptomic and epigenetic level. Our results provide fir ...[more]

PMID: 32737342

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DNA methylation profiling of epidermal tissue after acute repetitive irradiation

Project description:DNA methylation data generated from epidermal samples (suction blister roofs) of healthy female subjects after repetitive irradiation on three consecutive days using a full spectrum solar simulator. DNA was extracted from suction blisters taken from irradiated and control sites on the lower backs of each subject 24 hours after the final irradiation. DNA was bisulfite converted and then profiled using Illumina Infinium MethylationEPIC BeadChip arrays.

2020-09-02 | E-MTAB-9249 | biostudies-arrayexpress

Expression profiling of the aging epidermis [RNA seq]

Project description:Whole transcriptome sequencing data generated from epidermal samples (suction blister roofs) of healthy female subjects between 21 and 76 years. Aim of the project was the investigation of non-linearities in the human aging progression using an integrative multi-omics analysis. RNA was extracted from suction blisters taken from the volar forearms of each subject, cDNA converted and then sequenced on an Illumina HiSeq 2500 (single-end, 50 bp) to an approximate sequencing depth of 100 million reads per sample.

2020-07-24 | E-MTAB-8995 | biostudies-arrayexpress

Transcription profiling of rat testes to investigate the effects of radiation

Project description:Analysis of LBNF1 rat testes from controls, containing both somatic and all germ cell types and from irradiated rats in which all cells germ cells except type A spermatgogonia are eliminated. Results provide insight into distinguishing germ and somatic cell genes and identification of somatic cell genes that are upregulated after irradiation. Experiment Overall Design: We studied 10 Sample replicates of control rat testes and 5 Sample replicates of irradiated rat testes.

2009-10-10 | E-GEOD-15223 | biostudies-arrayexpress

T-cell lymphoblastic lymphomas induced by gamma-irradiation

Project description:This SuperSeries is composed of the following subset Series: GSE10858: Comparative Genomic hybridization of gamma-irradiated T-cell lymphomas GSE10859: Expression patterns of cDNAs in gamma-irradiation induced T-cell lymphomas GSE10891: Gamma-irradiation induced T-cell lymphomas (miRNA study) Keywords: SuperSeries Refer to individual Series

2010-05-26 | E-GEOD-10861 | biostudies-arrayexpress

Methylation profiling of the aging epidermis [450k]

Project description:DNA methylation array data generated from epidermal samples (suction blister roofs) of healthy female subjects between 21 and 76 years. Aim of the project was the investigation of non-linearities in the human aging progression using an integrative multi-omics analysis. DNA was extracted from suction blisters taken from the volar forearms of each subject, bisulfite converted, and profiled using Illumina Infinium HumanMethylation450 BeadChip arrrays.

2020-07-24 | E-MTAB-8992 | biostudies-arrayexpress

Methylation profiling of the aging epidermis [850k]

2020-07-24 | E-MTAB-8993 | biostudies-arrayexpress

Estrogen regulated genes in rat testes and their relationship to recovery of spermatogenesis after irradiation

Project description:Despite numerous observations of effects of estrogens on spermatogenesis, identification of estrogen-regulated genes in the testis is limited. We previously showed in rats, in which irradiation had completely blocked spermatogonial differentiation, that testosterone (T) suppression with GnRH-antagonist and antiandrogen stimulated spermatogenic recovery and addition of estradiol (E2) to this regimen accelerated this recovery. We report here the global changes in testicular cell gene expression induced by the E2 treatment. By minimizing the changes in other hormones and also having concurrent data on the regulation of the genes by those hormones, we were able to dissect the effects of estrogen on gene expression, independent of gonadotropin or T changes. Expression of 20 genes, largely in somatic cells, was up- or down-regulated between 2- and 5-fold by E2. There were also early germ cell genes whose expression increased but this was a result of a small increase in spermatogonial numbers. The striking enrichment of transcripts not corresponding to known genes among the E2-downregulated probes led to the identification of one as micro-RNA miR-34a. We propose that genes whose expression levels are altered in one direction by irradiation and in the opposite direction by both T suppression and E2 treatment are candidates for controlling the block in differentiation. Several genes, including insulin-like 3 (Insl3), satisfied those criteria. If they are indeed involved in the inhibition of spermatogonial differentiation, they may be candidate targets for clinical treatments to enhance recovery of spermatogenesis following gonadotoxic exposures, such as those resulting from cancer therapy. 6 sample replicates of hormonal ablation plus estradiol treatment, compared to previous 14 Sample replicates of sham treatment and 11 Sample replicates of hormonal ablation treatment groups in GSE15243

2011-11-22 | E-GEOD-24672 | biostudies-arrayexpress

Differential modification of the C. elegans proteome in response to acute and chronic gamma radiation: link with reproduction decline

Project description:Ecosystems are chronically exposed to ionizing radiations. But environmental risk assessment of chronic exposure suffers from a lack of knowledge. Extrapolation of data from acute to chronic exposure is not always relevant, and can lead to uncertainties. In fact, effects could be different between the two irradiation modes, especially regarding reproduction endpoint, which is an ecologically relevant parameter . The free living nematode Caenorhabditis elegans is a particularly appropriate model organism to address this proteomic issues. With its fully sequenced genome and its short life cycle, C. elegans has been successfully used to study acute and chronic irradiation effects and their consequences on germline development and hatching. Results showed that a decrease of the number of progeny associated with a decrease of hatching success occurred from and above 30 Gy of acute irradiation.. In the present study, we decided to refine the understanding of molecular mechanisms of acute and chronic irradiation by a global proteome analysis. To do so, C. elegans were exposed to 3 common cumulated doses between acute and chronic exposure. These 3 doses, lower than the doses for which an effect on the reproduction was shown, were susceptible to allow us to find early and sensitive biomarkers of a reproduction decline. After exposure, global modification of the proteome expression was studied using a label free LC-MS/MS proteomic approach. Our objectives were to test the following hypotheses: (1) whether or not proteome expression varied with the dose, and with the irradiation mode; (2) if proteome expression modification was associated with effects on reproduction, with potential direct implications for ecological risk assessment.

2020-10-15 | PXD011731 | Pride

Gene expression profile of bone marrow with post-irradiation radioprotector

Project description:To elucidate the mechanism of the in vivo radioprotection activity of Zn-containing heat-treated Saccharomyces cerevisiae yeast (Zn-yeast), expression changes in bone marrow after whole body irradiation (WBI) with concomitant treatment of Zn-yeast were analyzed using microarray technology. Keywords: mouse, bone marrow, Zn-containing heat-treated yeast administration, gamma-irradiation Zn-yeast suspension was administered i.p. into C3H mice immediately after 7.5 Gy WBI. Bone marrow from irradiated mice was extracted at 6 hours after irradiation and analyzed by microarray containing of 44,000 probes.

2010-09-27 | E-GEOD-18727 | biostudies-arrayexpress

Deciphering Diazirine Reaction Mechanism: through Irradiation Modulation for Residue-Specific Distance Restraints in Protein Photo-Crosslinking

Project description:The diazirine photoreactive group has been widely used for photo-labeling and photo-cross-linking (PXL) of proteins. Yet, due to the mechanistic complexity of diazirine photo-reaction, site-specific and quantitative analysis of protein PXL data remains challenging. Herein, we have built an in-line photo-reaction monitoring system, capable of systematically varying optical power density and irradiation time. Using this system, we have determined the kinetic parameters of diazirine photo-reactions, and shown that an alkyl diazirine undergoes rearrangement upon irradiation to yield a diazo intermediate. A carbene intermediate is produced from the diazo intermediate upon further irradiation, whereas at a relatively small proportion, it is produced directly from the diazirine. Both diazo and carbene intermediates react with protein side-chains. Significantly, the diazo intermediate preferentially reacts with polar side-chains, exhibiting much higher specificity than the carbene intermediate. As the diazo and carbene intermediates are generated sequentially, modulating irradiation time and optical power density can achieve site- or space- selective PXL results through different mechanisms. Together, we have established a new approach for the kinetic mechanism of photo-reactions, and paved the way for quantitative analysis of PXLs to visualize protein structure and dynamics.

2024-06-22 | PXD048452 | Pride

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