Julius Judd1, Fabiana M. Duarte1,2, and John T. Lis1
1Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14835, USA
2Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
This is a GitHub repository that contains supplemental data for the paper "Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription". Preprint: https://doi.org/10.1101/2020.05.10.087262 Raw data: GSE149336 (GEO) PRJNA627972 (SRA)
All code used for analysis can be found in the file "Supplemental_Code.Rmd", or in the accompanying pdf file.
Contains all DESeq2 differential expression testing output for all comparisions performed in the paper.
Contains bed format files, including macs2 peak calls for ATAC-seq and GAF ChIP-seq data, lists of GAF-bound genes with or without GAF-dependent pause signal, and lists of genes that are dependent on GAF and PBAP for pausing, only GAF, or only PBAP. Also included is a filtered list of PRO-cap corrected, unique dm6 transcripts that passed our upstream transcription filter.
Contains bigWig format files of data. ATAC-seq, PROseq, RNAseq, and CUTANDRUN data was generated for this paper. For each data type, there are bigWig files for raw, un-normalized signal (of individual replicates), and merged normalized tracks. RNA-seq and PRO-seq are normalized by spike-in control, and ATAC-seq was normalized using DESeq2 sizeFactors. ChIP-seq contains published data that was reanalyzed for this paper, either by realignment of raw data or by liftOver of signal tracks. M1BP PRO-seq contains published M1BP knockdown PRO-seq signal tracks that were lifted over to the dm6 genome assembly.
Contains a bed file of PRO-cap corrected dm6 genes.
The file "hub.txt" can be loaded at the UCSC genome browser here: https://genome.ucsc.edu/cgi-bin/hgHubConnect. Paste the raw url (https://raw.githubusercontent.com/JAJ256/GAF/master/hub.txt) and click "Add Hub".