Resources
-
Wong KW, Zeng Y, Tay E, Teo JHJ, Cipta NO, Hamashima K, Yi Y, Liu H, Warrier T, Le MTN, Ng SC, Li QJ, Li H, Loh YH
Nuclear receptor-SINE B1 network modulates expanded pluripotency in blastoids and blastocysts. Nat Commun.
2024 Nov 19;15(1):10011. doi: 10.1038/s41467-024-54381-0. PMID: 39562549; PMCID: PMC11577042.
GEO: RNA-seq: GSE210788; Single-cell RNA-seq: GSE210789 and GSE217826; ATAC-seq: GSE217825; ChIP-seq: GSE217824; WGBS: GSE244019.
-
Hamashima K, Wong KW, Sam TW, Teo JHJ, Taneja R, Le MTN, Li QJ, Hanna JH, Li H, Loh YH
Single-nucleus multiomic mapping of m6A methylomes and transcriptomes in native populations of cells with sn-m6A-CT. Mol Cell.
2023 Aug 25:S1097-2765(23)00649-4. doi: 10.1016/j.molcel.2023.08.010. Epub ahead of print. PMID: 37657444; PMCID: PMC10895704.
GEO : GSE217256
Code : The code for sn-m6A-CT data analysis is included as Methods S2 -
Warrier T, El Farran C, Zeng Y, Ho BSQ, Bao Q, Zheng ZH, Bi X, Ng HH, Ong DST, Chu JJH, Sanyal A, Fullwood MJ, Collins JJ, Li H, Xu J, Loh YH
SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. Nucleic Acids Res.
2022 Jul 22;50(13):7326-7349. doi: 10.1093/nar/gkac531. PMID: 35776115; PMCID: PMC9303280.
GEO : GSE123245
-
Gautam P, Hamashima K, Chen Y, Zeng Y, Makovoz B, Parikh BH, Lee HY, Lau KA, Su X, Wong RCB, Chan WK, Li H, Blenkinsop TA, Loh YH
Multi-species single-cell transcriptomic analysis of ocular compartment regulons. Nat Commun.
2021 Sep 28;12(1):5675. doi: 10.1038/s41467-021-25968-8. PMID: 34584087; PMCID: PMC8478974.
GEO : GSE147979 (human and pig eyes), GSE118480 (macaque retina cells), GSE63472 (mouse retina cells), GSE135406 (zebrafish retina cells), GSE137537 (human retina cells), and E-MTAB-7316 (human macula/periphery cells)
-
Xing QR, El Farran CA, Gautam P, Chuah YS, Warrier T, Toh CD, Kang NY, Sugii S, Chang YT, Xu J, Collins JJ, Daley GQ, Li H, Zhang LF, Loh YH
Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing. Sci Adv.
2020 Sep 11;6(37):eaba1190. doi: 10.1126/sciadv.aba1190. PMID: 32917699; PMCID: PMC7486102.
GEO : GSE100345
-
Fang HT, El Farran CA, Xing QR, Zhang LF, Li H, Lim B, Loh YH
Global H3.3 dynamic deposition defines its bimodal role in cell fate transition. Nat Commun.
2018 Apr 18;9(1):1537. doi: 10.1038/s41467-018-03904-7. PMID: 29670118; PMCID: PMC5906632.
GEO : GSE99592
-
Khattar E, Kumar P, Liu CY, AkŽñncŽñlar SC, Raju A, Lakshmanan M, Maury JJ, Qiang Y, Li S, Tan EY, Hui KM, Shi M, Loh YH, Tergaonkar V
Telomerase reverse transcriptase promotes cancer cell proliferation by augmenting tRNA expression. J Clin Invest.
2016 Oct 3;126(10):4045-4060. doi: 10.1172/JCI86042. Epub 2016 Sep 19. PMID: 27643433; PMCID: PMC5096818.
GEO : GSE77146 and GSE81509
-
Yang BX, El Farran CA, Guo HC, Yu T, Fang HT, Wang HF, Schlesinger S, Seah YF, Goh GY, Neo SP, Li Y, Lorincz MC, Tergaonkar V, Lim TM, Chen L, Gunaratne J, Collins JJ, Goff SP, Daley GQ, Li H, Bard FA, Loh YH
Systematic identification of factors for provirus silencing in embryonic stem cells. Cell.
2015 Sep 24;163(1):230-45. doi: 10.1016/j.cell.2015.08.037. Epub 2015 Sep 10. PMID: 26365490; PMCID: PMC4686136.
GEO : GSE70865