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Accession Number: GSE106334 Platform: GPL17021: Illumina HiSeq 2500 (Mus musculus) Organism: Mus musculus Published on 2018-01-03 Summary: This SuperSeries is composed of the SubSeries listed below. Overall Design: Refer to individual Series Contact: Name: Matthias Stadtfeld Organization: NYU School of Medicine Address: 540 First Avenue Skirball Lab 4-1 New York 10016 USA Organization: GEO Address: USA
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Accession Number: GSE108674 Platform: GPL16686: [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version] Organism: Homo sapiens Published on 2018-01-03 Summary: PGC-1s (PGC-1alpha and PGC-1beta) are transcriptional coactivators involved in mitochondrial biogenesis, metabolism, and antioxidant defense. Given the existing links between PGC-1s and aging, we wanted to investigate the contribution of PGC-1s to skin aging. Keratinocytes form a self-renewable layer that differentiate to generate full epidermis. Defects in keratinocyte metabolism related to aging or PGC-1s depletion could impair normal function of keratinocytes and contribute to skin thinning. We used microarrays to detail the global gene expression changes shared by the aging process and the depletion in PGC-1s. Overall Design: We selected a pair of primary keratinocytes from human donors that were matched for gender (male), ethnicity (caucasian) and body site (back skin). Young cells were from a 28 y.o. donor, aged cells were from a 83 y.o. (55-year difference). Cells were cultured using the same media and grown at similar cell densities. RNA were extracted from subconfluent cultures 3 days post-treatment (siRNA control or siRNA PGC-1alpha+PGC1beta). Each condition has 2 biological replicates. Contact: Name: Julie St-Pierre Organization: University of Ottawa Deparment: Department of Biochemistry, Microbiology and Immunology Address: 451 Smyth Rd Ottawa ON Canada Email: julie.st-pierre@uottawa.ca Organization: Affymetrix, Inc. Address: Santa Clara CA 95051 USA Email: geo@ncbi.nlm.nih.gov, support@affymetrix.com Phone: 888-362-2447 Web-Link: http://www.affymetrix.com/index.affx
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Accession Number: GSE99105 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2018-01-03 Summary: Deciphering the rules of genome folding in the cell nucleus is essential in order to understand its functions. Recent Hi-C studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus, or whether they reflect statistical frequencies of measured interactions within cell populations is unclear. Here, using a combination of Hi-C, 3D-Fluorescent In Situ Hybridization (3D-FISH), super-resolution microscopy and polymer modeling, we provide an integrative view of chromatin folding in Drosophila. We observed that repressed TADs form a succession of discrete nano-compartments, interspersed by less condensed active regions. Single-cell analysis revealed a consistent TAD-based physical compartmentalization of the chromatin fiber, with some degree of heterogeneity in intra-TAD conformations and in cis and trans inter-TAD contact events. These results indicate that TADs are fundamental 3D genome units that engage in dynamic higher-order inter-TAD connections. This domain-based architecture is likely to play a major role in regulatory transactions during DNA-dependent processes. Overall Design: HiC experiments in drosophila male embryos Contact: Name: Jia-Ming Chang Organization: National Chengchi University Deparment: Department of Computer Science Address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District Taipei 11605 Taiwan Email: chang.jiaming@gmail.com Organization: GEO Address: USA
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Accession Number: GSE80775 Platform: GPL13112: Illumina HiSeq 2000 (Mus musculus) Organism: Mus musculus Published on 2018-01-03 Summary: Induction of a protective response to oxidative stress, both from a transcriptional and from a genetic viewpoint, confers a selective advantage for cells exposed to an inflammatory environment, paving the way to neoplastic transformation Overall Design: Chromatin immuno-precipitations of acetylated lysine 27 of H3 followed by multiparallel sequencing, performed on tissues of Mdr2-WT (FVB.129P2) livers, Mdr2-KO (FVB.129P2-Abcb4tm1Bor/J) inflamed livers or hepatocarcinoma nodules from Mdr2-KO livers. All samples have been treated with clodronate liposomes to prevent sample contamination by liver macrophages Contact: Name: Alberto Termanini Organization: Istituto Clinico Humanitas Laboratory: GN Address: Via Manzoni, 113 Rozzano MI 20089 Italy Email: termanini@me.com Organization: GEO Address: USA
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Accession Number: GSE108495 Platform: GPL23227: BGISEQ-500 (Homo sapiens) Organism: Homo sapiens Published on 2018-01-03 Summary: This study is to identify downstream genes regulated by STAT3 in response cytosolic acidification. Dysregulated intracellular pH is emerging as a hallmark of cancer. In spite of their acidic environment, cancer cells maintain alkaline intracellular pH (≥7.4) that promotes cancer progression by inhibiting apoptosis and increasing glycolysis, cell growth, migration and invasion. Here, we identify signal transducer and activator of transcription 3 (STAT3) as a key player in the maintenance of alkaline cytosolic pH. STAT3 associates with the vacuolar H+-ATPase on lysosomal membranes in a coiled coil domain-dependent manner and increases its activity in living cells and in vitro. Accordingly, STAT3 depletion disrupts intracellular proton equilibrium by decreasing and increasing cytosolic and lysosomal pH, respectively. This dysregulation can be reverted by reconstitution with wild type STAT3 as well as STAT3 mutants unable to activate target genes (Tyr-705-Phe and DNA binding mutant) or to regulate mitochondrial respiration (Ser-727-Ala). Upon cytosolic acidification, phospho-Tyr-705-STAT3 is rapidly dephosphorylated, transcriptionally inactivated and further recruited to lysosomal membranes to reestablish intracellular proton equilibrium and to enhance cell survival. These data reveal STAT3 as a regulator of intracellular pH, and vice versa intracellular pH as a regulator of STAT3 localization and activity. Overall Design: Twelve samples in total have been analysed. HeLa WT is the control for HeLa STAT3 KO. HeLa blank is the control for PA+EIPA. Each group has 3 replicates. Contact: Name: Yonglun Luo Organization: Aarhus University Address: Wilhelm Meyers Allé 4 aarhus Denmark Email: yonglun.luo@hum-gen.au.dk Phone: 0045-89421666 Organization: GEO Address: USA
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Accession Number: GSE99106 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2018-01-03 Summary: Deciphering the rules of genome folding in the cell nucleus is essential in order to understand its functions. Recent Hi-C studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus, or whether they reflect statistical frequencies of measured interactions within cell populations is unclear. Here, using a combination of Hi-C, 3D-Fluorescent In Situ Hybridization (3D-FISH), super-resolution microscopy and polymer modeling, we provide an integrative view of chromatin folding in Drosophila. We observed that repressed TADs form a succession of discrete nano-compartments, interspersed by less condensed active regions. Single-cell analysis revealed a consistent TAD-based physical compartmentalization of the chromatin fiber, with some degree of heterogeneity in intra-TAD conformations and in cis and trans inter-TAD contact events. These results indicate that TADs are fundamental 3D genome units that engage in dynamic higher-order inter-TAD connections. This domain-based architecture is likely to play a major role in regulatory transactions during DNA-dependent processes. Overall Design: HiC experiments in ph mutant drosophila embryos Contact: Name: Jia-Ming Chang Organization: National Chengchi University Deparment: Department of Computer Science Address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District Taipei 11605 Taiwan Email: chang.jiaming@gmail.com Organization: GEO Address: USA
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Accession Number: GSE101956 Platform: GPL22761: Illumina MiSeq (Aedes aegypti) Organism: Aedes aegypti Published on 2018-01-03 Summary: We performed small RNA sequencing (Illumina MiSeq) of mosquito Aedes aegypti to profile expression of tRNA derived fragments. Overall Design: We sequenced small RNA libraries from different biological samples such as males and females from 5 Aedes aegypti lab strains, developmental stages of Moyo-S and Moyo-R strains,and Moyo-S and Moyo-R females after blood feeding. Contact: Name: Susanta K. Behura Organization: Univeristy of Missouri Deparment: Division of Animal Sciences Address: 920 East Campus Drive Columbia Missouri 65211 USA Email: behuras@missouri.edu Organization: GEO Address: USA
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Accession Number: GSE80776 Platform: GPL13112: Illumina HiSeq 2000 (Mus musculus) Organism: Mus musculus Published on 2018-01-03 Summary: Induction of a protective response to oxidative stress, both from a transcriptional and from a genetic viewpoint, confers a selective advantage for cells exposed to an inflammatory environment, paving the way to neoplastic transformation Overall Design: Sequencing of RNA extracted from tissues of Mdr2-WT (FVB.129P2) livers, Mdr2-KO (FVB.129P2-Abcb4tm1Bor/J) inflamed livers or hepatocarcinoma nodules from Mdr2-KO livers. All samples have been treated with clodronate liposomes to prevent sample contamination by liver macrophages Contact: Name: Alberto Termanini Organization: Istituto Clinico Humanitas Laboratory: GN Address: Via Manzoni, 113 Rozzano MI 20089 Italy Email: termanini@me.com Organization: GEO Address: USA
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Accession Number: GSE106107 Platform: GPL19057: Illumina NextSeq 500 (Mus musculus) Organism: Mus musculus Published on 2018-01-03 Summary: Tissue-resident memory CD8+ T cells (Trm) are positioned at common sites of pathogen exposure where they elicit rapid and robust protective immune responses. However, the molecular signals controlling Trm differentiation and homeostasis are not fully understood. Here we show that mouse Trm precursor cells represent a unique CD8+ T cell subset that is distinct from the precursors of circulating memory populations at the levels of gene expression and chromatin accessibility. Exploiting computational and functional RNAi in vivo screens, we identified the transcription factor (TF) Runx3 as a key regulator of Trm differentiation and homeostasis. Runx3 was required to establish Trm populations in diverse tissue environments and supported expression of critical tissue-residency genes while suppressing genes associated with tissue egress and recirculation. Analysis of the accessibility of Runx3 target genes in Trm-precursor cells revealed a distinct regulatory role for Runx3 in controlling Trm differentiation despite relatively widespread and uniform expression among all CD8+ T cell subsets. Further, we show that human and murine tumor-infiltrating lymphocytes (TIL) share a core tissue-residency gene-expression signature with Trm. In a mouse model of adoptive T cell therapy for melanoma, Runx3-deficient CD8+ TIL failed to accumulate in tumors, resulting in greater rates of tumor growth and mortality. Conversely, overexpression of Runx3 enhanced TIL abundance, delayed tumor growth, and prolonged survival. In addition to establishing Runx3 as a central regulator of Trm differentiation, these results provide novel insight into the signals that promote T cell residency in tissues, which could be leveraged to enhance vaccine efficacy or adoptive cell therapy treatments that target cancer. Overall Design: 6 samples, 2 replicates each, 2 wildtype controls. Contact: Name: Adam Getzler Organization: TSRI-FL Address: 130 Scripps Way Jupiter FL 33458-5284 USA Email: agetzler@scripps.edu Organization: GEO Address: USA
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Accession Number: GSE99107 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) GPL17275: Illumina HiSeq 2500 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2018-01-03 Summary: This SuperSeries is composed of the SubSeries listed below. Overall Design: Refer to individual Series Contact: Name: Jia-Ming Chang Organization: National Chengchi University Deparment: Department of Computer Science Address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District Taipei 11605 Taiwan Email: chang.jiaming@gmail.com Organization: GEO Address: USA
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