ktest_data_genome_biology_2024

This repository contains the reversion dataset and the scChIP-Seq dataset analysed in Ozier-Lafontaine et. al 2024. 

Files associated to reversion dataset : 

reversion_SCT_residuals.csv : Pearson residuals of the scRNAseq dataset based on the R package sctransform  

reversion_SCT_residuals_batch_corrected.csv : Batch-centered Pearson residuals of the scRNAseq dataset based on the R package sctransform  

RTqPCR_reversion_logx.csv : log(X+1) normalization of the RTqPCR dataset 

RTqPCR_reversion_logcentered.csv Batch-centered log(X+1) normalization of the RTqPCR dataset 

Files associated to the scChIP-Seq dataset : 

human_epdnew_qoQwV.bed 

MM468_H3K27me3_peaks_3000_10000_95_uncorrected_correlation_filtered.qs 

The scripts to perform the data analysis are on the github repository https://github.com/AnthoOzier/ktest_experiment_genome_biology_2024   

The reversion dataset comes from Zreika, S., Fourneaux, C., Vallin, E. et al. Evidence for close molecular proximity between reverting and undifferentiated cells. BMC Biol 20, 155 (2022). https://doi.org/10.1186/s12915-022-01363-7

本仓库收录了Ozier-Lafontaine等人2024年研究中所分析的逆转数据集（reversion dataset）与单细胞染色质免疫沉淀测序（single-cell Chromatin Immunoprecipitation Sequencing, scChIP-Seq）数据集。

逆转数据集关联文件如下：
reversion_SCT_residuals.csv：基于R包sctransform的单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）数据集的皮尔逊残差
reversion_SCT_residuals_batch_corrected.csv：基于R包sctransform的scRNA-seq数据集的批次中心化皮尔逊残差
RTqPCR_reversion_logx.csv：逆转录实时定量聚合酶链反应（Reverse Transcription Quantitative Polymerase Chain Reaction, RT-qPCR）数据集的log(X+1)归一化处理结果
RTqPCR_reversion_logcentered.csv：RT-qPCR数据集的批次中心化log(X+1)归一化处理结果

单细胞染色质免疫沉淀测序数据集关联文件如下：
human_epdnew_qoQwV.bed
MM468_H3K27me3_peaks_3000_10000_95_uncorrected_correlation_filtered.qs

本研究的数据分析脚本托管于GitHub仓库：https://github.com/AnthoOzier/ktest_experiment_genome_biology_2024

本逆转数据集源自Zreika S、Fourneaux C、Vallin E等人的研究成果，该研究发表于《BMC Biology》2022年第20卷第155篇文章，文章标题为《逆转细胞与未分化细胞间的紧密分子关联性证据》，DOI链接：https://doi.org/10.1186/s12915-022-01363-7