# Datasets associated with the manuscript "Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution", by Roscito,Sameith,Parra et al. 2017. # The subdirectories contain all genome/mRNA/ATAC sequencing datasets and ATAC-seq peaks generated for this study. ########################################## ### TEGU LIZARD GENOME SEQUENCING DATA ### ########################################## ### # directory: tegu_genome_MiSeqs #Paired-end MiSeq sequencing libraries; raw data L4594_Track-9543_teguGenomeMiSeq_R1.fastq L4594_Track-9543_teguGenomeMiSeq_R2.fastq L4975_Track-10365_teguGenomeMiSeq_R1.fastq L4975_Track-10365_teguGenomeMiSeq_R2.fastq L4975_Track-11218_teguGenomeMiSeq_R1.fastq L4975_Track-11218_teguGenomeMiSeq_R2.fastq L4975_Track-11280_teguGenomeMiSeq_R1.fastq L4975_Track-11280_teguGenomeMiSeq_R2.fastq L5486_Track-12221_teguGenomeMiSeq_R1.fastq L5486_Track-12221_teguGenomeMiSeq_R2.fastq L5486_Track-12423_teguGenomeMiSeq_R1.fastq L5486_Track-12423_teguGenomeMiSeq_R2.fastq ### # directory: tegu_genome_HiSeqs #Mate pairs HiSeq sequencing libraries; raw data #2Kb libraries L4141_Track-10093_teguGenomeHiSeq_R1.fastq L4141_Track-10093_teguGenomeHiSeq_R2.fastq L4141_Track-13200_teguGenomeHiSeq_R1.fastq L4141_Track-13200_teguGenomeHiSeq_R2.fastq L4142_Track-10094_teguGenomeHiSeq_R1.fastq L4142_Track-10094_teguGenomeHiSeq_R2.fastq #10Kb libraries L4620_Track-10095_teguGenomeHiSeq_R1.fastq L4620_Track-10095_teguGenomeHiSeq_R2.fastq L4719_Track-10096_teguGenomeHiSeq_R1.fastq L4719_Track-10096_teguGenomeHiSeq_R2.fastq ######################################## ### TEGU LIZARD mRNA SEQUENCING DATA ### ######################################## ### # directory: tegu_mRNA #Paired-end 75 bp, strand-specific HiSeq sequencing libraries; raw data L5208_Track-11224_tegumRNA_R1.fastq L5208_Track-11224_tegumRNA_R2.fastq L5209_Track-11225_tegumRNA_R1.fastq L5209_Track-11225_tegumRNA_R2.fastq L5210_Track-11226_tegumRNA_R1.fastq L5210_Track-11226_tegumRNA_R2.fastq L5211_Track-11227_tegumRNA_R1.fastq L5211_Track-11227_tegumRNA_R2.fastq L5212_Track-11228_tegumRNA_R1.fastq L5212_Track-11228_tegumRNA_R2.fastq L5213_Track-11229_tegumRNA_R1.fastq L5213_Track-11229_tegumRNA_R2.fastq L5214_Track-11230_tegumRNA_R1.fastq L5214_Track-11230_tegumRNA_R2.fastq L5215_Track-11231_tegumRNA_R1.fastq L5215_Track-11231_tegumRNA_R2.fastq ######################## ### TEGU LIZARD ATAC ### ######################## ### # directory: tegu_ATAC #Paired-end 75 bp sequencing libraries; raw data L6331_Track-15261_teguBrainRep1_R1.fastq L6331_Track-15261_teguBrainRep1_R2.fastq L6332_Track-15262_teguLimbRep1_R1.fastq L6332_Track-15262_teguLimbRep1_R2.fastq L6333_Track-15263_teguLimbRep2_R1.fastq L6333_Track-15263_teguLimbRep2_R2.fastq L8160_Track-22725_teguBrainRep2_R1.fastq L8160_Track-22725_teguBrainRep2_R2.fastq L8161_Track-22726_teguLimbRep3_R1.fastq L8161_Track-22726_teguLimbRep3_R2.fastq L8162_Track-22727_teguLimbRep4_R1.fastq L8162_Track-22727_teguLimbRep4_R2.fastq L8163_Track-21471_teguFlankRep1_R1.fastq L8163_Track-21471_teguFlankRep1_R2.fastq L8164_Track-21472_teguFlankRep2_R1.fastq L8164_Track-21472_teguFlankRep2_R2.fastq L8165_Track-21473_teguHeartRep1_R1.fastq L8165_Track-21473_teguHeartRep1_R2.fastq L8166_Track-21474_teguHeartRep2_R1.fastq L8166_Track-21474_teguHeartRep2_R2.fastq L8167_Track-21475_teguLiverRep1_R1.fastq L8167_Track-21475_teguLiverRep1_R2.fastq L8168_Track-21476_teguLiverRep2_R1.fastq L8168_Track-21476_teguLiverRep2_R2.fastq L8169_Track-21477_teguBrainRep3_R1.fastq L8169_Track-21477_teguBrainRep3_R2.fastq L8170_Track-21478_teguBrainRep4_R1.fastq L8170_Track-21478_teguBrainRep4_R2.fastq L8171_Track-21479_teguEmbryoRep1_R1.fastq L8171_Track-21479_teguEmbryoRep1_R2.fastq L8172_Track-21480_teguEmbryoRep2_R1.fastq L8172_Track-21480_teguEmbryoRep2_R2.fastq #macs2 narrowPeak files L6331_Track-15261_teguBrainRep1.narrowPeak L6332_Track-15262_teguLimbRep1.narrowPeak L6333_Track-15263_teguLimbRep2.narrowPeak L8160_Track-22725_teguBrainRep2.narrowPeak L8161_Track-22726_teguLimbRep3.narrowPeak L8162_Track-22727_teguLimbRep4.narrowPeak L8163_Track-21471_teguFlankRep1.narrowPeak L8164_Track-21472_teguFlankRep2.narrowPeak L8165_Track-21473_teguHeartRep1.narrowPeak L8166_Track-21474_teguHeartRep2.narrowPeak L8167_Track-21475_teguLiverRep1.narrowPeak L8168_Track-21476_teguLiverRep2.narrowPeak L8169_Track-21477_teguBrainRep3.narrowPeak L8170_Track-21478_teguBrainRep4.narrowPeak L8171_Track-21479_teguEmbryoRep1.narrowPeak L8172_Track-21480_teguEmbryoRep2.narrowPeak ################## ### MOUSE ATAC ### ################## ### # directory: mouse_ATAC #Paired-end 75 bp sequencing libraries; raw data L5143_Track-11219_mouseMidbrainE115rep1_R1.fastq L5143_Track-11219_mouseMidbrainE115rep1_R2.fastq L5144_Track-11220_mouseMidbrainE115rep2_R1.fastq L5144_Track-11220_mouseMidbrainE115rep2_R2.fastq L5145_Track-11221_mouseLimbE115rep1_R1.fastq L5145_Track-11221_mouseLimbE115rep1_R2.fastq L5146_Track-11222_mouseLimbE115rep2_R1.fastq L5146_Track-11222_mouseLimbE115rep2_R2.fastq L5147_Track-11223_mouseLimbE115rep3_R1.fastq L5147_Track-11223_mouseLimbE115rep3_R2.fastq L8173_Track-21137_mouseWholeEyeE115rep1_R1.fastq L8173_Track-21137_mouseWholeEyeE115rep1_R2.fastq L8174_Track-21138_mouseWholeEyeE115rep2_R1.fastq L8174_Track-21138_mouseWholeEyeE115rep2_R2.fastq L8177_Track-21141_mouseRetinaE145rep1_R1.fastq L8177_Track-21141_mouseRetinaE145rep1_R2.fastq L8178_Track-21142_mouseRetinaE145rep2_R1.fastq L8178_Track-21142_mouseRetinaE145rep2_R2.fastq L8179_Track-21143_mouseLensE145rep1_R1.fastq L8179_Track-21143_mouseLensE145rep1_R2.fastq L8180_Track-21144_mouseLensE145rep2_R1.fastq L8180_Track-21144_mouseLensE145rep2_R2.fastq #macs2 narrowPeak files L5143_Track-11219_mouseMidbrainE115rep1.narrowPeak L5144_Track-11220_mouseMidbrainE115rep2.narrowPeak L5145_Track-11221_mouseLimbE115rep1.narrowPeak L5146_Track-11222_mouseLimbE115rep2.narrowPeak L5147_Track-11223_mouseLimbE115rep3.narrowPeak L8173_Track-21137_mouseWholeEyeE115rep1.narrowPeak L8174_Track-21138_mouseWholeEyeE115rep2.narrowPeak L8177_Track-21141_mouseRetinaE145rep1.narrowPeak L8178_Track-21142_mouseRetinaE145rep2.narrowPeak L8179_Track-21143_mouseLensE145rep1.narrowPeak L8180_Track-21144_mouseLensE145rep2.narrowPeak