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Resource: A single-cell transcriptome atlas of the maturing zebrafish telencephalon
- Shristi Pandey,
- Anna J. Moyer,
- and Summer B. Thyme
Genome Res. April 2023 33: 658-671; Published in Advance April 18, 2023, doi:10.1101/gr.277278.122
...signatures of the neuronal cell types in the telencephalon and the timeline of their emergence from larva to adult remain largely undescribed. Using an integrated analysis of single-cell transcriptomes of approximately 64,000 cells obtained from 6-day-postfertilization (dpf), 15-dpf, and adult telencephalon...
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Research: Cellular age explains variation in age-related cell-to-cell transcriptome variability
- Ming Yang,
- Benjamin R. Harrison,
- and Daniel E.L. Promislow
Genome Res. November 2023 33: 1906-1916; Published in Advance November 16, 2023, doi:10.1101/gr.278144.123
...: promislo@uw.eduAbstractOrgans and tissues age at different rates within a single individual. Such asynchrony in aging has been widely observed at multiple levels, from functional hallmarks, such as anatomical structures and physiological processes, to molecular endophenotypes, such as the transcriptome...
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Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
- Stephanie M. Zimmerman,
- Robin Fropf,
- Bridget R. Kulasekara,
- Maddy Griswold,
- Oliver Appelbe,
- Arya Bahrami,
- Rich Boykin,
- Derek L. Buhr,
- Kit Fuhrman,
- Margaret L. Hoang,
- Quoc Huynh,
- Lesley Isgur,
- Andrew Klock,
- Alecksandr Kutchma,
- Alexa E. Lasley,
- Yan Liang,
- Jill McKay-Fleisch,
- Jeffrey S. Nelson,
- Karen Nguyen,
- Erin Piazza,
- Aric Rininger,
- Daniel R. Zollinger,
- Michael Rhodes,
- and Joseph M. Beechem
Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
..., preserving the spatial and morphological context of gene expression. Here, we describe expanding the chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
..., University of Copenhagen, DK-2100 Copenhagen 2200, Denmark; 11Evolutionary and Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou 310058, China ↵12 These authors contributed equally to this work. Corresponding authors: tomas.marques@upf.edu, david.juan@upf.edu, guojiezhang@zju.edu.cnAbstractTranscriptomic...
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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
....calarco@utoronto.caAbstractAlternative splicing plays a major role in shaping tissue-specific transcriptomes. Among the broad tissue types present in metazoans, the central nervous system contains some of the highest levels of alternative splicing. Although many documented examples of splicing differences between broad tissue types exist...
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Research: Transcriptome evidence reveals enhanced autophagy-lysosomal function in centenarians
- Fu-Hui Xiao,
- Xiao-Qiong Chen,
- Qin Yu,
- Yunshuang Ye,
- Yao-Wen Liu,
- Dongjing Yan,
- Li-Qin Yang,
- Guijun Chen,
- Rong Lin,
- Liping Yang,
- Xiaoping Liao,
- Wen Zhang,
- Wei Zhang,
- Nelson Leung-Sang Tang,
- Xiao-Fan Wang,
- Jumin Zhou,
- Wang-Wei Cai,
- Yong-Han He,
- and Qing-Peng Kong
Genome Res. November 2018 28: 1601-1610; Published in Advance October 23, 2018, doi:10.1101/gr.220780.117
...contributed equally to this work. Corresponding authors: kongqp@mail.kiz.ac.cn, heyonghan@mail.kiz.ac.cn, caiww591020@163.com, zhoujm@mail.kiz.ac.cnAbstractCentenarians (CENs) are excellent subjects to study the mechanisms of human longevity and healthy aging. Here, we analyzed the transcriptomes of 76...
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Resource: Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
- Ekaterina Khrameeva,
- Ilia Kurochkin,
- Dingding Han,
- Patricia Guijarro,
- Sabina Kanton,
- Malgorzata Santel,
- Zhengzong Qian,
- Shen Rong,
- Pavel Mazin,
- Marat Sabirov,
- Matvei Bulat,
- Olga Efimova,
- Anna Tkachev,
- Song Guo,
- Chet C. Sherwood,
- J. Gray Camp,
- Svante Pääbo,
- Barbara Treutlein,
- and Philipp Khaitovich
Genome Res. May 2020 30: 776-789; Published in Advance May 18, 2020, doi:10.1101/gr.256958.119
...expression within brain regions and compare homologous cell types across species (La Manno et al. 2016; Saunders et al. 2018; Tosches et al. 2018; Zeisel et al. 2018). A single-cell level comparison between human and macaque transcriptomes in prenatal and adult dorsolateral prefrontal cortices indeed showed...
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Method: Massively parallel cis-regulatory analysis in the mammalian central nervous system
- Susan Q. Shen,
- Connie A. Myers,
- Andrew E.O. Hughes,
- Leah C. Byrne,
- John G. Flannery,
- and Joseph C. Corbo
Genome Res. February 2016 26: 238-255; Published in Advance November 17, 2015, doi:10.1101/gr.193789.115
...of assayedCREs and bywidening the repertoire of assayable cell types. The retina and cerebral cortex are two parts of the central nervous system (CNS) with a shared forebrain origin, whose gene regulatory networks are topics of intense research interest (Swaroop et al. 2010; Wright et al. 2010; Bae et al...
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Resource: Improved definition of the mouse transcriptome via targeted RNA sequencing
- Giovanni Bussotti,
- Tommaso Leonardi,
- Michael B. Clark,
- Tim R. Mercer,
- Joanna Crawford,
- Lorenzo Malquori,
- Cedric Notredame,
- Marcel E. Dinger,
- John S. Mattick,
- and Anton J. Enright
Genome Res. May 2016 26: 705-716; doi:10.1101/gr.199760.115
...Improved definition of the mouse transcriptome via targeted RNA sequencing Giovanni Bussotti 1 , 7 , Tommaso Leonardi 1 , Michael B. Clark 2 , 3 , Tim R. Mercer 2 , 4 , Joanna Crawford 5 , Lorenzo Malquori 5 , Cedric...
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Method: Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome
- Hagen Tilgner,
- Fereshteh Jahanbani,
- Ishaan Gupta,
- Paul Collier,
- Eric Wei,
- Morten Rasmussen,
- and Michael Snyder
Genome Res. February 2018 28: 231-242; Published in Advance December 1, 2017, doi:10.1101/gr.230516.117
...LLC, Menlo Park, California 94025, USA ↵4 These authors contributed equally to this work. Corresponding authors: hagen.u.tilgner@gmail.com, mpsnyder@stanford.eduAbstractUnderstanding transcriptome complexity is crucial for understanding human biology and disease. Technologies such as Synthetic long...
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