Supplemental Data for 'Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription'

Julius Judd¹, Fabiana M. Duarte^1,2, 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)

Analysis code

All code used for analysis can be found in the file "Supplemental_Code.Rmd", or in the accompanying pdf file.

Data

DESeq_results

Contains all DESeq2 differential expression testing output for all comparisions performed in the paper.

Bed

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.

bw

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.

Genome

Contains a bed file of PRO-cap corrected dm6 genes.

UCSC trackhub

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".