Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

The uploaded files are source datasets for the scMTNI algorithm. scMTNI is a multi-task learning framework that integrates the cell lineage structure, scRNA-seq and scATAC-seq measurements to enable joint inference of cell type-specific GRNs. See more details at Zhang, S., Pyne, S., Pietrzak, S. et al. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. Nat Commun 14, 3064 (2023). https://doi.org/10.1038/s41467-023-38637-9 The source data scMTNI_sourcedata.tar.gz contains the following 3 parts: 1) The cluster-specific scRNA-seq matrices and the prior networks for all three datasets and scMTNI inferred consensus networks. 2) Gold standard human and mouse datasets for evaluation. 3) Source data for scMTNI figures 2-8 and supplementary figures. The key for each figure and its corresponding file path is in SourceData_Key_v2.xlsx. The source data Buenrostro_Hematopoiesis.tar.gz contains the scRNA-seq data for human hematopoietic differentiation downloaded from Data S2 of Buenrostro et al. The source data RawMotifFiles.tar.gz contains the motif instance files and promoter files for human and mouse for generating prior networks using scATAC-seq data for scMTNI. Check https://github.com/Roy-lab/scMTNI/blob/master/Scripts/genPriorNetwork/readme.md for examples and scripts. The Buenrostro_priorNetwork_bamfiles.tar.gz contains the raw bam files of scATAC-seq data for human hematopoietic differentiation downloaded from Buenrostro et al.

本次上传的文件均为scMTNI算法的源数据集。scMTNI是一款多任务学习框架，可整合细胞谱系结构、单细胞RNA测序（single-cell RNA sequencing，scRNA-seq）与单细胞转座酶可及性测序（single-cell assay for transposase-accessible chromatin using sequencing，scATAC-seq）数据，实现细胞类型特异性基因调控网络（Gene Regulatory Networks，GRNs）的联合推断。相关详细信息可参阅论文：Zhang S, Pyne S, Pietrzak S, et al. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. *Nature Communications*, 2023, 14: 3064. https://doi.org/10.1038/s41467-023-38637-9

本次提供的源数据集scMTNI_sourcedata.tar.gz包含以下三部分内容：
1. 三个数据集各自的聚类特异性scRNA-seq表达矩阵、先验网络，以及scMTNI算法推断得到的共识网络；
2. 用于模型评估的人类与小鼠金标准数据集；
3. scMTNI算法生成图2至图8及补充图所需的源数据。
每张图对应的检索密钥与文件路径均收录于SourceData_Key_v2.xlsx文件中。

源数据集Buenrostro_Hematopoiesis.tar.gz包含从Buenrostro等人补充材料S2中获取的人类造血分化过程scRNA-seq数据。

源数据集RawMotifFiles.tar.gz包含人类与小鼠的基序实例文件及启动子文件，用于基于scATAC-seq数据为scMTNI算法生成先验网络。相关示例与脚本可参阅：https://github.com/Roy-lab/scMTNI/blob/master/Scripts/genPriorNetwork/readme.md

源数据集Buenrostro_priorNetwork_bamfiles.tar.gz包含从Buenrostro等人处获取的人类造血分化过程scATAC-seq数据原始BAM格式文件。