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  • Accession Number: GSE101861 Platform: GPL5642: 3D-Gene Mouse Oligo chip 24k Organism: Mus musculus Published on 2018-01-03 Summary: Transcriptional profiling of mouse lung tissues. C57BL/6J mice were airway-specifically transfected with betaENaC to generate betaENaC-Tg mice. Overall Design: Two-condition experiment, WT vs. ENaC-Tg cells of lung tissues. Biological replicates: One replicate per array. Contact: Name: Satoshi Kondo Organization: Toray Industries,Inc. Deparment: New Projects Development Division Address: Tebiro 6-10-1 Kamakura Kanagawa Japan Email: Satoshi_Kondou@nts.toray.co.jp Name: Satoko Takizawa Organization: TORAY Industries, Inc. Deparment: New Frontiers Research Laboratories Address: 6-10-1 Tebiro Kamakura Kanagawa Japan Email: Toray3D-Gene@nts.toray.co.jp Phone: +81-467-32-9351
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  • Accession Number: GSE107871 Platform: GPL10999: Illumina Genome Analyzer IIx (Homo sapiens) Organism: Homo sapiens Published on 2018-01-03 Summary: Keratinocyte (KC) hyper-proliferation and epidermal thickening are characteristic features of psoriasis lesions, but the specific contributions of KCs to plaque formation are not fully understood. This study used RNA-seq to investigate the transcriptome of primary monolayer KC cultures grown from lesional (PP) and non-lesional (PN) biopsies of psoriasis patients and control subjects (NN). Whole skin biopsies from the same subjects were evaluated concurrently. RNA-seq analysis of whole skin identified a larger number of psoriasis-increased differentially expressed genes (DEGs), but analysis of KC cultures identified more PP- and PN-decreased DEGs. These latter DEG sets overlapped more strongly with genes near loci identified by psoriasis genome-wide association studies and were enriched for genes associated with epidermal differentiation. Consistent with this, the frequency of AP-1 motifs was elevated in regions upstream of PN-KC-decreased DEGs. A subset of these genes belonged to the same co-expression module, mapped to the epidermal differentiation complex, and exhibited differentiation-dependent expression. These findings demonstrate a decreased differentiation gene signature in PP/PN-KCs that had not been identified by pre-genomic studies of patient-derived monolayers. This may reflect intrinsic defects limiting psoriatic KC differentiation capacity, which may contribute to compromised barrier function in normal-appearing uninvolved psoriatic skin. Overall Design: Samples were obtained from lesional skin of psoriasis patients (PP), uninvolved skin of psoriasis patients (PN), and normal skin from control individuals (NN). RNA was extracted from full-thickness skin biopsies of keratinocytes (KCs) grown as monolayer cutures. Samples were obtained from 4 psoriasis patients (individuals 1 - 4) and 4 control subjects (individuals 5 - 8). Contact: Name: William R Swindell Organization: University of Michigan Deparment: Dermatology Address: 1500 E. Medical Center Drive Ann Arbor MI 48104 USA Email: wswindel@umich.edu Organization: GEO Address: USA
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  • Accession Number: GSE106332 Platform: GPL17021: Illumina HiSeq 2500 (Mus musculus) Organism: Mus musculus Published on 2018-01-03 Summary: The ability of induced pluripotent stem cells (iPSCs) to differentiate into all adult cell types makes them attractive for basic research and regenerative medicine applications, but it remains unknown when and how this hallmark of the pluripotent state is established. Here, we pinpoint the acquisition of developmental pluripotency in a suitable reprogramming system and show that nascent iPSCs abruptly and without extensive maturation period in culture become capable of generating all tissues upon injection into preimplantation embryos. Strikingly, the developmental potential of nascent iPSCs is comparable to or even surpasses that of high-quality established pluripotent cells. Further functional assays as well as genome-wide transcriptional and chromatin analyses suggest that cells acquiring developmental pluripotency exhibit a unique combination of molecular and functional properties that distinguish them from canonical pluripotency states. These include reduced clonal self-renewal potential and the elevated expression of transcriptional regulators of postimplantation development. Our observations close an important gap in our understanding of induced pluripotency and provide an improved roadmap of cellular reprogramming with ramifications for the biomedical use of iPSCs. Overall Design: RNA-seq cells at four stages of reprogramming (MEF, Stage 1 or day 6, Stage 2 or day 6+4 and established iPSCs) in triplicate. Cells (except MEFs) were sorted for Oct4-GFP+ 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: GSE102042 Platform: GPL6244: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] Organism: Homo sapiens Published on 2018-01-03 Summary: Analysis of gene expression profiling of cultured skin fibroblasts obtained from patients affected with vascular Ehlers Danlos syndrome (vEDS) Transcriptome-wide expression profiling using the Affymetrix Gene 1.0 ST platform comparing the gene expression pattern of cultured skin fibroblasts derived from three patients with vEDS with those of nine healthy individuals Overall Design: Comparison of transcriptome profiling of human cultured skin fibroblasts from three vEDS patients and nine healthy individuals Contact: Name: Nicola Chiarelli Organization: University of Brescia Deparment: Molecular and Translational Medicine Address: Viale Europa 11 Brescia 25100 Italy Email: nicola.chiarelli@unibs.it Phone: +390303717261 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: GSE90742 Platform: GPL19057: Illumina NextSeq 500 (Mus musculus) Organism: Mus musculus Published on 2018-01-03 Summary: The classical tenet of hematopoiesis posits well-accepted lineage trees that arise from progressively restricted oligopotent and unipotent progenitor populations. However, because fate in hematopoiesis has mostly been studied in the context of transplantation, it is unclear whether these lineage branches and such proposed oligopotent progenitors exist in an unperturbed hematopoietic system. Here, we utilize endogenous transposon tagging to trace the fate of thousands of progenitors and stem cells over time to re-evaluate these dogmas. Our results describe a novel clonal roadmap where the megakaryocyte lineage arises independently of lymphoid and myeloid/erythroid fates. Our data also demonstrate that true oligopotency is largely restricted to the multipotent progenitor (MPP) compartment. Analysis of thousands of stem cell and progenitor transcriptomes demonstrates that lineage determination starts at the MPP stage and identifies a functional hierarchy within this population that drives hematopoiesis. Finally, our results demonstrate that long-term hematopoietic stem cells behave physiologically as megakaryocyte lineage progenitors. Our data provide evidence for a substantially revised hematopoietic roadmap, and highlights unique properties of MPPs and HSCs in situ. Overall Design: Single-cell mRNA sequencing of hematopoietic stem cells and multipotent progenitor subsets from mouse bone marrow. Sample LTHSC represents 940 single cells. Sample MPP2 represents 776 single cells. Sample MPP3 represents 1372 single cells. Sample MPP4 represents 1016 single cells. Sample STHSC represents 837 single cells. Contact: Name: Fernando Camargo Organization: Boston Children's Hospital Deparment: Stem Cell and Regenerative Biology Address: 300 Longwood Ave Boston MA 02115 USA Email: Fernando.Camargo@childrens.harvard.edu Organization: GEO Address: USA
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  • Accession Number: GSE101072 Platform: GPL23682: Illumina HiSeq 2500 (Clytia hemisphaerica) Organism: Clytia hemisphaerica Published on 2018-01-03 Summary: We aimed to quantify in silico the expression level of candidate genes in different Clytia gonad tissues and oocytes at different growth stage Overall Design: A total of 8 samples were analysed: 4 different gonad samples; 2 biological replicates for each. In order to obtain a high enough RNA concentration for each sample we pooled tissues and oocytes that had been dissected in different days, under the same conditions and same jellyfish age. Contact: Name: Evelyn Houliston Organization: Sorbonne Universités, UPMC Univ. Paris 06, CNRS Laboratory: LBDV (UMR7009) Address: chemin du Lazaret Villefranche-sur-mer 06230 France Email: houliston@obs-vlfr.fr Organization: GEO Address: USA
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  • Accession Number: GSE100092 Platform: GPL11154: Illumina HiSeq 2000 (Homo sapiens) Organism: Homo sapiens Published on 2018-01-03 Summary: Cancer cells exploit the epithelial-to-mesenchymal transition (EMT) program toward metastasis. Cytoskeletal regulators are dually required in mesenchymal cells by promoting EMT-induced migration and sustaining the EMT program itself. In search for novel regulators of metastasis, we conducted an shRNA screen targeting a class of microtubule regulators, the plus-end tracking proteins (+TIPs). We show that the +TIP ACF7 is required for both the maintenance of EMT and to promote migration. We identified HectD1 as a potent E3 ubiquitin ligase mediating ACF7 degradation. Depletion of HectD1 robustly increases ACF7 protein levels and this is sufficient to enhance migration and EMT in cells, as well as facilitate metastasis in vivo. Ours results report the HectD1/ACF7 axis as a novel regulator of metastasis of breast cancer cells. Overall Design: Differential gene expression profile following ACF7 overexpression or Hetd1 depletion by RNA sequencing (Illumina HiSEq 2500) Contact: Name: Stephanie Duhamel Organization: IRCM Address: 110 avenue des pins ouest montreal Quebec Canada Email: stephanie.duhamel@ircm.qc.ca Organization: GEO Address: USA
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  • Accession Number: GSE100813 Platform: GPL11154: Illumina HiSeq 2000 (Homo sapiens) Organism: Homo sapiens Published on 2018-01-03 Summary: Peptidyl-prolyl isomerases (PPIs) are a superfamily of ubiquitous enzymes that catalyze the cis-trans interconversion of Xaa-Pro peptide bonds. The functions of most PPIs remain uncharacterized. FKBP25, a mammalian PPI, localizes to the nucleus, binds nucleic acids, and associates with chromatin modifying enzymes. However, the role of this protein in transcriptional regulation remains unclear. To help address this question we present RNA-seq gene expression profiling in HEK293 cells transfected with siRNA targeting FKBP25 relative to a GFP-targeting negative control. Overall Design: Human embryonic kidney cells (HEK 293) were transfected with siRNA targeting FKBP25 or a GFP-targeting negative control and incubated for 72 h. Cells were harvested with trypsin, pelleted, and flash frozen before mRNA purification using the µMACs mRNA isolation kit (Miltenyl Biotec, Bergisch Gladbach, Germany). Purified mRNA was then analysed on an Agilent 2100 Bioanalyzer using Agilent 6000 RNA Nano Kit (Agilent Technologies, Santa Clara, California). cDNA was generated using the Superscript Double-Stranded cDNA Synthesis kit (ThermoFisher), 75bp paired-end libraries prepared using the Paired-End Sample Prep Kit (Illumina, San Diego, California) and then sequenced on a HiSeq 2000 sequencing system (Illumina). Contact: Name: Christopher J Nelson Organization: University of Victoria Laboratory: Nelson Deparment: Biochemistry & Microbiology Address: 3800 Finnerty Rd Victoria British Columbia Canada Email: cjn@uvic.ca Phone: 250-853-3889 Organization: GEO Address: USA
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  • Accession Number: GSE97993 Platform: GPL17021: Illumina HiSeq 2500 (Mus musculus) Organism: Mus musculus Published on 2018-01-03 Summary: Myeloid-derived suppressor cells (MDSC) are potent negative regulators of immune responses at many pathological conditions. It is widely accepted that these cells are not present under steady state condition. Here, we report that MDSC with highly potent ability to suppress T cells accumulate during first two weeks of life in mice. MDSC suppressive activity in neonates was triggered by lactoferrin, a component of milk, and mediated by nitric oxide and up-regulation of PGE2 regulated by S100A9/A8 proteins. Newborn MDSC had transcriptome similar to that of tumor MDSC. However, they had strong up-regulation of antimicrobial gene network. This was associated with enhanced antimicrobial activity of these cells. MDSC played a critical role in control of experimental necrotizing enterocolitis in newborn mice. In humans, MDSC in cord blood of low-weight preterm infants prone to the development of NEC had significantly lower suppressive activity than the cells from cord blood of infants with normal weight. Thus, transitory presence of MDSC after birth is critical for the maintenance of immune homeostasis. Overall Design: RNA-seq on PMN-MDSC and M-MDSC cells from adult and neonate mice Contact: Name: Priyankara J Wickramasinghe Organization: The Wistar Institute Laboratory: Genomics Deparment: Bioinformatics Address: 3601 Spruce Street Philadelphia PA 19104 USA Email: priyaw@wistar.org Phone: 2154956837 Organization: GEO Address: USA
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  • Accession Number: GSE99104 Platform: GPL17275: Illumina HiSeq 2500 (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 S2R+ cells 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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