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Greene, Dongbo Hu<!-- -->, <!-- --> <!-- -->Richard W. W. Jones<!-- -->, <!-- --> <!-- -->Stephanie Liu<!-- -->, <!-- --> <!-- -->David S. Mejia<!-- -->, <!-- --> <!-- -->Rob Patro<!-- -->, <!-- --> <!-- -->Stephen R. Piccolo<!-- -->, <!-- --> <!-- -->Ariel Rodriguez Romero<!-- -->, <!-- --> <!-- -->Hirak Sarkar<!-- -->, <!-- --> <!-- -->Candace L. Savonen<!-- -->, <!-- --> <!-- -->Jaclyn N. Taroni<!-- -->, <!-- --> <!-- -->William E. Vauclain<!-- -->, <!-- --> <!-- -->Deepashree Venkatesh Prasad<!-- -->, <!-- --> <!-- -->Kurt G. Wheeler<!-- -->, <!-- --> <!-- -->Arkadii Yakovets<!-- -->, <!-- --> <!-- -->Nozomi Ichihara<!-- -->.<!-- --> <strong>refine.bio: a resource of uniformly processed publicly available gene expression datasets.</strong></span><span class="StyledText-sc-1sadyjn-0 kixbWF">URL:<!-- --> <a target="_blank" rel="nofollow" class="StyledAnchor-sc-1rp7lwl-0 ijUisb Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="https://www.refine.bio">https://www.refine.bio</a></span>
1<p class="StyledParagraph-sc-tbetod-0 heOyEn"><i>Note that the contributor list is in alphabetical order as we prepare a manuscript for submission</i></p></div></div></div><div class="StyledBox-sc-13pk1d4-0 gvWrBN"><div class="StyledBox-sc-13pk1d4-0 fQMCWK"><a class="StyledAnchor-sc-1rp7lwl-0 dbJkVu Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="/license">BDS 3-Clause License</a><div class="StyledBox__StyledBoxGap-sc-13pk1d4-1 hbAHdy"></div><a class="StyledAnchor-sc-1rp7lwl-0 dbJkVu Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="/privacy">Privacy</a><div class="StyledBox__StyledBoxGap-sc-13pk1d4-1 hbAHdy"></div><a class="StyledAnchor-sc-1rp7lwl-0 dbJkVu Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="/terms">Terms of Use</a><div class="StyledBox__StyledBoxGap-sc-13pk1d4-1 hbAHdy"></div><a class="StyledAnchor-sc-1rp7lwl-0 dbJkVu Anchor__CustomAnchor-sc-14ibwp4-0 gmiraL" href="mailto:[email protected]">Contact</a></div><div class="StyledBox-sc-13pk1d4-0 faiElH"><span class="StyledText-sc-1sadyjn-0 jsgMtg">Version <!-- -->1.46.22<!-- --> - <!-- -->.0.0</span></div></div></div></footer><div style="bottom:5vh;display:none;position:fixed;right:5vw;z-index:4" class="StyledBox-sc-13pk1d4-0 gyhkwO"><div tabindex="0" role="button" style="box-shadow:none" class="StyledBox-sc-13pk1d4-0 fDSRyR"><div style="position:relative;transform:rotate(-45deg)" class="StyledBox-sc-13pk1d4-0 lbAbcj BackToTopButton__ArrowIcon-sc-bourn0-0 hCljmS"></div><span class="StyledText-sc-1sadyjn-0 irCqcv"><strong>Back to Top</strong></span></div></div><div id="portal" class="StyledBox-sc-13pk1d4-0 bjWreY"></div></div></div></div>
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How progenitors and their daughter cells are temporally patterned remains unknown. Here, we trace the transcriptional trajectories of successive generations of apical progenitors (APs) and isochronic cohorts of their daughter neurons in the developing mouse neocortex using high temporal resolution parallel single-cell RNA sequencing. We identify and functionally characterize a core set of evolutionarily-conserved temporally patterned genes which drive APs from internally-driven states to more exteroceptive states, revealing a progressively increasing role for extracellular signals as corticogenesis unfolds. These embryonic age-dependent AP molecular states are reflected in their neuronal progeny as successive ground states, onto which essentially conserved early post-mitotic differentiation programs are applied. Thus, temporally unfolding molecular birthmarks present in progenitors act in their post-mitotic progeny as seeds for adult neuronal diversity. Overall design: Investigation of the transcriptional dynamics in time-locked cohorts of cortical cells across embryonic neurogenesis. Flashtag is injected at 4 ages (E12, E13, E14, E15), and cells collected 1H, 24H, 96H after birth (= a total of 12 conditions) and analyzed by single cell transcriptomics.","technology":"RNA-SEQ","accession_code":"SRP158666","alternate_accession_code":"GSE118953","submitter_institution":"","has_publication":true,"publication_doi":"","publication_authors":["Telley L","Agirman G","Prados J","Amberg N","Fièvre S","Oberst P","Bartolini G","Vitali I","Cadilhac C","Hippenmeyer S","Nguyen L","Dayer A","Jabaudon D"],"sample_metadata_fields":["subject"],"platform_names":["Illumina HiSeq 2500"],"platform_accession_codes":["IlluminaHiSeq2500"],"organism_names":["MUS_MUSCULUS"],"downloadable_organism_names":["MUS_MUSCULUS"],"pubmed_id":"31073041","num_total_samples":2756,"num_processed_samples":2756,"num_downloadable_samples":2756,"source_first_published":"2019-05-11T00:00:00+00:00"},{"id":65064,"title":"Spatio-temporal transcriptome of the human brain","publication_title":"Spatio-temporal transcriptome of the human brain.","description":"The development of the human brain is a complex and precisely regulated process that unfolds over a protracted period of time. Human-specific features of this process, especially the ways in which highly complex neural circuits of the cerebral cortex form, are likely to be important factors in the evolution of human specializations. However, in addition to giving us remarkable cognitive and motor abilities, the formation of intricate neural circuits may have also increased our susceptibility to psychiatric and neurodegenerative disorders. Furthermore, substantial evidence suggests that the symptoms and progression of many brain disorders are dramatically influenced by genetic and developmental processes that define regional cell phenotypes and connectivity. Sex differences also play an important role in brain development and function and are a risk factor for several brain disorders, such as autism spectrum disorders (ASD) and depression. Thus understanding the spatiotemporal dynamics and functional organization of the brain transcriptome is essential to teasing out the keys to human neurodevelopment, sexual dimorphism, and evolution as well as our increased susceptibility to certain brain disorders.  Most transcriptome studies of the developing brain have been restricted to rodents, and those performed in humans and nonhuman primates have included relatively small sample sizes and predominantly focused on few regions or developmental time points. Because many prominent features of human brain development significantly diverge from those of well-characterized model organisms, the translation of knowledge across species is difficult, and it is likely that many underlying genetic processes have gone undetected. In this study, we have taken a genome-wide approach to analyze the human transcriptome at single-exon resolution with ~1.4 million exon-level probe set
1s in 16 brain regions from donors representing both sexes and multiple ethnicities, across pre and postnatal development, including adolescence, and adulthood. We also generated genome-wide genotype data for 2.5 million single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) for each specimen. Our analyses of the data revealed several features of the human brain transcriptome: spatiotemporal expression dynamics of individual and functionally related groups of genes, differential exon usage, sex-specific expression patterns and exon usage, and organization of the transcriptome into functional modules. We also profiled developmental trajectories of genes important for neurobiological themes and genes associated with ASD and schizophrenia. Finally, we present associations between specific SNPs and gene expression levels in different brain regions across development. The dataset presented here provides research opportunities and a wealth of information not previously available to the scientific community.","technology":"MICROARRAY","accession_code":"GSE25219","alternate_accession_code":"E-GEOD-25219","submitter_institution":"Yale University","has_publication":false,"publication_doi":"","publication_authors":["Kang HJ","Kawasawa YI","Cheng F","Zhu Y","Xu X","Li M","Sousa AM","Pletikos M","Meyer KA","Sedmak G","Guennel T","Shin Y","Johnson MB","Krsnik Z","Mayer S","Fertuzinhos S","Umlauf S","Lisgo SN","Vortmeyer A","Weinberger DR","Mane S","Hyde TM","Huttner A","Reimers M","Kleinman JE","Sestan N"],"sample_metadata_fields":["sex","age"],"platform_names":["[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]"],"platform_accession_codes":["HuEx-1_0-st"],"organism_names":["HOMO_SAPIENS"],"downloadable_organism_names":["HOMO_SAPIENS"],"pubmed_id":"22031440","num_total_samples":2680,"num_processed_samples":2667,"num_downloadable_samples":2667,"source_first_published":"2010-11-09T00:00:00+00:00"},{"id":61636,"title":"IMI MARCAR Project: towards novel biomarkers for cancer risk assessment","publication_title":"Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice.","description":"This SuperSeries is composed of the SubSeries listed below.","technology":"MICROARRAY","accession_code":"GSE68387","alternate_accession_code":"E-GEOD-68387","submitter_institution":"Novartis","has_publication":false,"publication_doi":"","publication_authors":["Lempiäinen H","Müller A","Brasa S","Teo SS","Roloff TC","Morawiec L","Zamurovic N","Vicart A","Funhoff E","Couttet P","Schübeler D","Grenet O","Marlowe J","Moggs J","Terranova R"],"sample_metadata_fields":["sex","age","specimen_part","treatment","subject","time"],"platform_names":["[RaGene-2_0-st] Affymetrix Rat Gene 2.0 ST Array","[Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array","[RAE230A] Affymetrix Rat Expression 230A Array","[HT_HG-U133_Plus_PM] Affymetrix HT HG-U133+ PM Array Plate","[Rat230_2] Affymetrix Rat Genome 230 2.0 Array","[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array"],"platform_accession_codes":["mouse430a2","ragene20st","hthgu133pluspm","mouse4302","rae230a","rat2302"],"organism_names":["MUS_MUSCULUS","HOMO_SAPIENS","RATTUS_NORVEGICUS"],"downloadable_organism_names":["MUS_MUSCULUS","HOMO_SAPIENS","RATTUS_NORVEGICUS"],"pubmed_id":"21455306","num_total_samples":2666,"num_processed_samples":1938,"num_downloadable_samples":1938,"source_first_published":"2015-04-29T00:00:00+00:00"},{"id":62525,"title":"Expression data measured by Nanostring and microarray of monocyte-derived dendritic cells from healthy individuals stimulated with LPS, influenza, or IFN-beta, or left unstimulated","publication_title":"Common genetic variants modulate pathogen-sensing responses in human dendritic cells.","description":"This SuperSeries is composed of the SubSeries listed below.","technology":"MICROARRAY","accession_code":"GSE57542","alternate_accession_code":"E-GEOD-57542","submitter_institution":"Broad Institute","has_publication":false,"publication_doi":"","publication_authors":["Lee MN","Ye C","Villani AC","Raj T","Li W","Eisenhaure TM","Imboywa SH","Chipendo PI","Ran FA","Slowikowski K","Ward LD","Raddassi K","McCabe C","Lee MH","Frohlich IY","Hafler DA","Kellis M","Raychaudhuri S","Zhang F","Stranger BE","Benoist CO","De Jager PL","Regev A","Hacohen N"],"sample_metadata_fields":["sex","age","race","subject"],"platform_names":["[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array"],"platform_accession_codes":["hugene10st"],"organism_names":["HOMO_SAPIENS"],"downloadable_organism_names":["HOMO_SAPIENS"],"pubmed_id":"24604203","num_total_samples":2554,"
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