Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Detection of circadian gene expression in human epidermal suction blister samples

ABSTRACT: To detect time of day dependent gene expression in human epidermis suction blister samples from 20 healthy subjects were obtained at three different time points throughout the day. RNA from 20 subjects were used to perform whole genome microarray analysis. Microarrays from 19 subjects showed sufficient quality to perform analysis for differential gene expression. We detected significant differential expression levels for several canonical clock genes such as Per1, Per2, Per3, Bmal1 and Rev-Erb_alpha throughout the day. In total we identified 294 genes that showed significant circadian gene expression including several transcription factors and rate limiting enzymes. To our knowledge this is the first study to investigate genome wide circadian gene expression in human epidermis. Suction blisters of human epidermis were obtained by applying a vacuum for approximately 2.5 h. Suction blisters for each subject (19 subjects in total) were harvested at 9.30 am, 2.30 pm and 7.30 pm.

ORGANISM(S): Homo sapiens

SUBMITTER: Florian Spoerl

PROVIDER: E-GEOD-35635 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Krüppel-like factor 9 is a circadian transcription factor in human epidermis that controls proliferation of keratinocytes.

Spörl Florian F Korge Sandra S Jürchott Karsten K Wunderskirchner Minetta M Schellenberg Katja K Heins Sven S Specht Aljona A Stoll Claudia C Klemz Roman R Maier Bert B Wenck Horst H Schrader Annika A Kunz Dieter D Blatt Thomas T Kramer Achim A

Proceedings of the National Academy of Sciences of the United States of America 20120618 27

Circadian clocks govern a wide range of cellular and physiological functions in various organisms. Recent evidence suggests distinct functions of local clocks in peripheral mammalian tissues such as immune responses and cell cycle control. However, studying circadian action in peripheral tissues has been limited so far to mouse models, leaving the implication for human systems widely elusive. In particular, circadian rhythms in human skin, which is naturally exposed to strong daytime-dependent c ...[more]

PMID: 22711835

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Project description:The goal of the experiment was to perform a large scale study of circadian regulation of gene expression in maize. To identify maize genes with expression regulated by the circadian clock, transcript levels in the aerial tissues of young maize seedlings were determined by transcriptional profiling with the Affymetrix GeneChip Maize Genome Array. Maize inbred B73 seedlings were grown inside Conviron growth chamber. B73 seedlings were grown for 7 days under 12 h light:12 h dark (LD) photocycles, 26° C temperature and 70% humidity. At the 8th day, seedlings were transferred to continuous light (LL) and were allowed to entrain completely for 24 h prior to tissue harvest following which tissue was harvested every 4 hours under LL conditions for a period of 48h. Therefore, for the circadian LL time course 12 time points were collected as follows (also defined as factors in the treatment section): ZT0 - 8:00 am/ subjective dawn/ Day1 ZT4 - 12:00 pm/ subjective mid-day/ Day1 ZT8 - 4:00 pm/ subjective late-day/ Day1 ZT12 - 8:00 pm/ subjective dusk/ Day1 ZT16 - 12:00 am/ subjective mid-night/ Day1 ZT20 - 4:00 am/ subjective pre-dawn/ Day1 ZT24- 8:00 am/ subjective dawn/ Day2 ZT28 - 12:00 pm/ subjective mid-day/ Day2 ZT32 - 4:00 pm/ subjective late-day/ Day2 ZT36 - 8:00 pm/ subjective dusk/ Day2 ZT40 - 12:00 am/ subjective mid-night/ Day2 ZT44 - 4:00 am/ subjective pre-dawn/ Day2 Tissue comprised of aerial portion of the seedlings (corresponding to tissue from the prop roots and up) for RNA isolation. Total RNA was isolated from the entire aerial portion of 7 day-old seedlings (corresponding to tissue from the prop roots and up) by Trizol extraction followed by Qiagen RNeasy columns and treatment with RNase-free DNase I (Qiagen; qiagen.com). RNA was isolated from 3 independent biological replicates was pooled. cRNA was generated from pooled total RNA from 3 biological replicates with the GeneChip One-Cycle Target Labeling kit according to the manufacturer’s recommendations (Affymetrix, affymetrix.com). The University of California, Berkeley Functional Genomics Laboratory hybridized samples to Affymetrix GeneChip Maize Genome Arrays and scanned the washed arrays as suggested by manufacturer. Probe sets called “Not Present” or “Marginal” on one or more microarrays were removed from the downstream analysis, as is common practice with circadian studies. Raw hybridization intensities were normalized across all twelve arrays using RMA express in Perfect Match mode. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Frank G. Harmon. The equivalent experiment is ZM28 at PLEXdb.]

Dataset Information

Detection of circadian gene expression in human epidermal suction blister samples

Publications

Krüppel-like factor 9 is a circadian transcription factor in human epidermis that controls proliferation of keratinocytes.

Similar Datasets

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