Advance and Application of Single-cell Transcriptomics in Auditory Research

Chadha S, Kamenov K, Cieza A. The world report on hearing, 2021. Bull World Health Organ 2021, 99: 242-242A.

Article  PubMed  PubMed Central  Google Scholar 

Basch ML, Brown RM II, Jen HI, Groves AK. Where hearing starts: The development of the mammalian cochlea. J Anat 2016, 228: 233–254.

Article  PubMed  Google Scholar 

Müller U, Barr-Gillespie PG. New treatment options for hearing loss. Nat Rev Drug Discov 2015, 14: 346–365.

Article  PubMed  Google Scholar 

Driver EC, Kelley MW. Development of the cochlea. Development 2020, 147: dev162263.

Hedlund E, Deng Q. Single-cell RNA sequencing: Technical advancements and biological applications. Mol Aspects Med 2018, 59: 36–46.

Article  CAS  PubMed  Google Scholar 

Hu Y, Zhang Y, Liu Y, Gao Y, San T, Li X. Advances in application of single-cell RNA sequencing in cardiovascular research. Front Cardiovasc Med 2022, 9: 905151.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cao Y, Zhu S, Yu B, Yao C. Single-cell RNA sequencing for traumatic spinal cord injury. FASEB J 2022, 36: e22656.

Article  PubMed  Google Scholar 

Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 2009, 6: 377–382.

Article  CAS  PubMed  Google Scholar 

Su M, Pan T, Chen QZ, Zhou WW, Gong Y, Xu G, et al. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res 2022, 9: 68.

PubMed  PubMed Central  Google Scholar 

Ramsköld D, Luo S, Wang YC, Li R, Deng Q, Faridani OR, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol 2012, 30: 777–782.

Article  PubMed  PubMed Central  Google Scholar 

Picelli S, Faridani OR, Björklund AK, Winberg G, Sagasser S, Sandberg R. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 2014, 9: 171–181.

Article  CAS  PubMed  Google Scholar 

Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 2015, 161: 1202–1214.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang X, Li T, Liu F, Chen Y, Yao J, Li Z, et al. Comparative analysis of droplet-based ultra-high-throughput single-cell RNA-seq systems. Mol Cell 2019, 73: 130-142.e5.

Article  PubMed  Google Scholar 

Adan A, Alizada G, Kiraz Y, Baran Y, Nalbant A. Flow cytometry: Basic principles and applications. Crit Rev Biotechnol 2017, 37: 163–176.

Article  CAS  PubMed  Google Scholar 

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-seq (MACS). Genome Biol 2008, 9: R137.

Article  PubMed  PubMed Central  Google Scholar 

García Alonso D, Yu M, Qu H, Ma L, Shen F. Advances in microfluidics-based technologies for single cell culture. Adv Biosyst 2019, 3: e1900003.

Article  PubMed  Google Scholar 

Dai X, Cai L, He F. Single-cell sequencing: Expansion, integration and translation. Brief Funct Genomics 2022, 21: 280–295.

Article  CAS  PubMed  Google Scholar 

Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, et al. Integrated analysis of multimodal single-cell data. Cell 2021, 184: 3573-3587.e29.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, et al. SCENIC: Single-cell regulatory network inference and clustering. Nat Methods 2017, 14: 1083–1086.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, et al. Reversed graph embedding resolves complex single-cell trajectories. Nat Methods 2017, 14: 979–982.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Efremova M, Vento-Tormo M, Teichmann SA, Vento-Tormo R. Cell PhoneDB: Inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat Protoc 2020, 15: 1484–1506.

Article  CAS  PubMed  Google Scholar 

Orvis J, Gottfried B, Kancherla J, Adkins RS, Song Y, Dror AA, et al. gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration. Nat Methods 2021, 18: 843–844.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Burns JC, Kelly MC, Hoa M, Morell RJ, Kelley MW. Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear. Nat Commun 2015, 6: 8557.

Article  CAS  PubMed  Google Scholar 

Hoa M, Olszewski R, Li X, Taukulis I, Gu S, DeTorres A, et al. Characterizing adult cochlear supporting cell transcriptional diversity using single-cell RNA-seq: Validation in the adult mouse and translational implications for the adult human cochlea. Front Mol Neurosci 2020, 13: 13.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Waldhaus J, Durruthy-Durruthy R, Heller S. Quantitative high-resolution cellular map of the organ of corti. Cell Rep 2015, 11: 1385–1399.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ranum PT, Goodwin AT, Yoshimura H, Kolbe DL, Walls WD, Koh JY, et al. Insights into the biology of hearing and deafness revealed by single-cell RNA sequencing. Cell Rep 2019, 26: 3160-3171.e3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Qian F, Wei G, Gao Y, Wang X, Gong J, Guo C, et al. Single-cell RNA-sequencing of zebrafish hair cells reveals novel genes potentially involved in hearing loss. Cell Mol Life Sci 2022, 79: 385.

Article  CAS  PubMed  Google Scholar 

Janesick A, Scheibinger M, Benkafadar N, Kirti S, Ellwanger DC, Heller S. Cell-type identity of the avian cochlea. Cell Rep 2021, 34: 108900.

Article  CAS  PubMed  Google Scholar 

Wang S, Lee MP, Jones S, Liu J, Waldhaus J. Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data. Genome Res 2021, 31: 1885–1899.

Article  PubMed  PubMed Central  Google Scholar 

Aleksiūnienė B, Matulevičiūtė R, Matulevičienė A, Burnytė B, Krasovskaja N, Ambrozaitytė L, et al. Opposite chromosome constitutions due to a familial translocation t(1;21)(q43;q22) in 2 cousins with development delay and congenital anomalies: A case report. Medicine (Baltimore) 2017, 96: e6521.

Article  PubMed  Google Scholar 

Kolla L, Kelly MC, Mann ZF, Anaya-Rocha A, Ellis K, Lemons A, et al. Characterization of the development of the mouse cochlear epithelium at the single cell level. Nat Commun 2020, 11: 2389.

Article  PubMed  PubMed Central  Google Scholar 

Weir FW, Hatch JL, Muus JS, Wallace SA, Meyer TA. Audiologic outcomes in ehlers-danlos syndrome. Otol Neurotol 2016, 37: 748–752.

Article  PubMed  Google Scholar 

Xu Z, Tu S, Pass C, Zhang Y, Liu H, Diers J, et al. Profiling mouse cochlear cell maturation using 10 × Genomics single-cell transcriptomics. Front Cell Neurosci 2022, 16: 962106.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jean P, Wong Jun Tai F, Singh-Estivalet A, Lelli A, Scandola C, Megharba S, et al. Single-cell transcriptomic profiling of the mouse cochlea: An atlas for targeted therapies. Proc Natl Acad Sci U S A 2023, 120: e2221744120.

Article  PubMed  PubMed Central  Google Scholar 

Campos-Barros A, Amma LL, Faris JS, Shailam R, Kelley MW, Forrest D. Type 2 iodothyronine deiodinase expression in the cochlea before the onset of hearing. Proc Natl Acad Sci U S A 2000, 97: 1287–1292.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ng L, Goodyear RJ, Woods CA, Schneider MJ, Diamond E, Richardson GP, et al. Hearing loss and retarded cochlear development in mice lacking type 2 iodothyronine deiodinase. Proc Natl Acad Sci U S A 2004, 101: 3474–3479.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ng L, Liu Y, Liu H, Forrest D. Cochlear fibrocyte and osteoblast lineages expressing type 2 deiodinase identified with a Dio2CreERt2 allele. Endocrinology 2021, 162: bqab179.

Article  PubMed  PubMed Central 

留言 (0)

沒有登入
gif