Various files for download from the vision project.

DNAsegs280_Ttfxn_mm10_bed.txt
	Custom track of tested enhancers with response category, red is enhancer, orange is threshold, blue is not an enhancer.

ErythReglRegMouse_ref_2017.xlsx
	Spreadsheet of known erythroid regulatory elements

GATA1_G1EER4_replicatesCombined_peaks_bed_mm10.txt	
	GATA1 peaks from our paper "Dynamics of the epigenetic landscape...". It is lifted over from mm9 to mm10.

blacklist
        Folder with files containing blacklist regions for the mouse mm10 build.

RNA/rnaHtseqCounts.txt
        File with the read counts from htseq for use with differential expression.  Each column is a separate replicate, each row is a gene.

RNA/rnaHtseqCountsall.0.txt
	Same as one above, only includes G1E and ER4.

RNA/rnaHtseqCounts_withcoordinates.txt
	This has rnaHtseqCounts.txt with gene coordinates added.  Header has
column definitions.

RNA/rnaHtseqCountsall_withcoordinates.0.txt
	Same as one above, only includes G1E and ER4.

RNA/rnaTPM_withcoordinates.txt
	This has the counts from rnaHtseqCounts.txt changed to TPMs via
	Transcripts = counts / length-of-gene
	TPM = Transcripts / sum(Transcripts) * 1,000,000

RNA/rnaHtseqCountsall_withcoordinates.0.txt
	Same as one above, only includes G1E and ER4.

RNA/scriptseq3.v3.tab
        File with expression levels (TPM) from RSEM.  Each column is a separate replicate, each row is a gene.  These come from the same alignments as the rnaHtseqCounts.txt.

gencode.vM4-tRNAs-ERCC.gtf
	Gene set used for the scriptseq3.v3.tab file.

atac_commonbgfdr01.bw
atac_commonpkfdr01.bw
	Regions of genome with ATAC signal used as peaks or background in common
	with all the cell types used for this IDEAS run.

IDEAShumanHem
	Directory containing a run of the S3V2-IDEAS-ESMP pipeline on mm10
	for comparison with the Human VISION run.

IDEASmouseHem2019
	Directory containing a run of the S3V2-IDEAS-ESMP pipeline on mm10

ideasJointFeb2021
	Directory containing a run of the S3V2-IDEAS-ESMP pipeline on mm10 from Feb 2021

ideasJointMay2021
	Directory containing a run of the S3V2-IDEAS-ESMP pipeline on mm10 from May 2021