This repository contains summarised data and analysis files for MEF cell reprogramming experiments. All genomic coordinate information contained in these files refers to the UCSC mm10 reference genome.
A UCSC browser session for the data generated in this study can be accessed through this link: Knaupp et. al. UCSC browser session
Folder containing all ATAC-seq peak call files.
/ATACseq/processed_data/ATAC_peaks/merged_replicate_peaks
File containing the read counts for ATAC-seq libraries in the union ATAC-seq peak set.
/ATACseq/processed_data/ATAC_peaks/atac_all_peaks_union_counts.txt
File containing the read counts for ChIP-seq libraries in the union ATAC-seq peak set.
/ATACseq/processed_data/ATAC_peaks/atac_all_peaks_union_os_chip_counts.txt
Folder containing BED files for ATAC-seq c-means clusters. Also contains folders for Homer2 motif enrichment results for each c-means cluster.
/ATACseq/processed_data/atac_cluster_peaks/c_means_peaks
Please note that the cluster numbers for the BED files are different to the cluster numbers indicated in the manuscript. Cluster number != Manuscript number. 1=2, 2=6, 3=4, 4=7, 5=1, 6=3, 7=5, 8=8.
Folder containing the ChIP-seq peak call files generated by MACS2.
/ChIPseq/processed_data/macs_output/merged_replicate_peak_calls
File containing the raw read counts for each gene.
/RNAseq/processed_data/polo_mm_iPSC_RNAseq_mm10_UCSC_gene_counts.txt
File containing the TPM normalised expression data.
/RNAseq/processed_data/polo_mm_iPSC_RNAseq_mm10_UCSC_TPM.txt
File containing sample id mapping for the above files.
/RNAseq/processed_data/sample_ids.txt
File containing differential expression results for SSEA1+ vs Thy1+ cells at day 6 of reprogramming. /RNAseq/processed_data/d6_thy_vs_ssea_DE_genes.txt