Surag Nair

Sep 22, 2024 | biorxiv.org | Avantika Lal |Laura M Gunsalus |Surag Nair |Tommaso Biancalani

AbstractDeep learning models are increasingly being used to perform a variety of tasks on DNA sequences, such as predicting tissue- and cell type- specific sequence activity, deriving cis-regulatory rules, predicting non-coding variant effects, and designing synthetic regulatory sequences. However, these models require specialized knowledge to build, train and interpret correctly.

Oct 21, 2023 | biorxiv.org | Surag Nair |Mohamed Ameen |Laksshman Sundaram |Anusri Pampari

AbstractEctopic expression of OCT4, SOX2, KLF4 and MYC (OSKM) transforms differentiated cells into induced pluripotent stem cells. To refine our mechanistic understanding of reprogramming, especially during the early stages, we profiled chromatin accessibility and gene expression at single-cell resolution across a densely sampled time course of human fibroblast reprogramming.

Oct 4, 2023 | biorxiv.org | Surag Nair |Mohamed Ameen |Laksshman Sundaram |Anusri Pampari

AbstractEctopic expression of OCT4, SOX2, KLF4 and MYC (OSKM) transforms differentiated cells into induced pluripotent stem cells. To refine our mechanistic understanding of reprogramming, especially during the early stages, we profiled chromatin accessibility and gene expression at single-cell resolution across a finely sampled time course of human fibroblast reprogramming.

Jul 13, 2023 | nature.com | Brian Zhong |Eric Sun |Surag Nair |Anshul Kundaje |Alexander Dunn

Laboratory animalsFor in vivo ATAC-seq libraries, an equal number of male and female GFAP-GFP (FVB/N background) mice32 were pooled and used. For ATAC-seq libraries generated from cultured NSCs, the SVZs from one male and one female C57BL/6 mouse obtained from the National Institute on Aging (NIA) Aged Rodent colony were pooled and used. For gene knockout experiments, male and female Rosa26-Cas9 knock-in mice116 (C57BL/6 background) were used (https://www.jax.org/strain/024858/).