Additional file 8: Table S2. of Reversing chromatin accessibility differences that distinguish homologous mitotic metaphase chromosomes

CNV and gene expression data in context of regions with DA and equivalent accessibility. Single copy probe locations of regions with DA (in bold) and equivalent accessibility (i.e. without DA) are from indicated GRCh37 genomic coordinates. Overlapping CNVs in the population from Healthy Sample (HS) and Ontario Population Genomics Platform (OPGP) are separated by a “//.” No recurrent CNVs (diploid copy number state) were observed in regions overlapped by single copy probes, and are indicated by a “0”. A 179 kb gain in region of single copy probe within C9orf66 was seen in only 1 out of ~400 HS individuals. This observation is a rare CNV and the region in which it resides, does not exhibit DA. SC probe locations do not overlap locations of CNVs reported in cell line GM06326 (see methods). GM10958 cell line CNV data have not been analyzed by genomic microarray analysis. This cell line has been characterized as phenotypically normal (Coriell Cell Repository). Compared to other tissues, mRNA abundance among human lymphocytes cells (EBV transformed, n = 54 individuals) showed low or no expression (most values below 0 on log10 scale, Genotype-Tissue Expression – GTEx database) for each of the single copy probes tested. C9orf66 expression was not catalogued in GTEx. The EMBL expression atlas (Illumina body map, http://www.ebi.ac.uk/gxa/experiments/E-MTAB-513) confirmed that it is not expressed in leukocytes. Marks of transcriptionally active chromatin (i.e. H3K36me3, H4K20me1 - reported values represent integrated intensities) were not significantly present (p = 0.91) in either DA (in bold, μ = 170.86) or equivalent accessible genomic regions (μ = 161.15). Integrated intensity values were processed from ENCODE ChIP-seq data on lymphoblastoid cell line GM12878 using the Broad histone signal intensity ‘StdSig’ setting within the UCSC Genome Table browser.

本数据集包含差异染色质可及性（Differential Accessibility, DA）区域及等效染色质可及性区域相关的拷贝数变异（Copy Number Variation, CNV）与基因表达数据。差异染色质可及性区域（以粗体标注）及等效染色质可及性区域（即无差异染色质可及性区域）的单拷贝探针位点均基于标注的GRCh37基因组坐标确定。来自健康样本（Healthy Sample, HS）与安大略人群基因组学平台（Ontario Population Genomics Platform, OPGP）的人群中重叠拷贝数变异以“//”分隔。在单拷贝探针覆盖的区域中未观察到复发性拷贝数变异（二倍体拷贝数状态），此类情况以“0”标注。在C9orf66区域内的单拷贝探针区域中，仅在约400名健康样本个体中的1名检测到179 kb的片段扩增。该变异为罕见拷贝数变异，其所在区域未表现出差异染色质可及性。单拷贝（Single Copy, SC）探针位点与GM06326细胞系中报道的拷贝数变异位点无重叠（详见方法部分）。GM10958细胞系的拷贝数变异数据尚未通过基因组微阵列分析进行检测。该细胞系经Coriell细胞库（Coriell Cell Repository）鉴定为表型正常细胞系。相较于其他组织，在经EB病毒转化的人类淋巴细胞（样本量n=54名个体）中，所检测的所有单拷贝探针对应的基因在该组织中均呈低表达或不表达（绝大多数数值在log10尺度下小于0，数据来自基因型组织表达（Genotype-Tissue Expression, GTEx）数据库）。GTEx数据库中未收录C9orf66的表达数据。欧洲分子生物学实验室表达图谱（Illumina人体图谱，http://www.ebi.ac.uk/gxa/experiments/E-MTAB-513）证实，C9orf66在白细胞中无表达。在差异染色质可及性区域（以粗体标注，均值μ=170.86）及等效染色质可及性基因组区域（均值μ=161.15）中，转录活跃染色质标记物（即H3K36me3、H4K20me1，报道数值为整合强度）均未呈现显著富集（p=0.91）。整合强度数值源自淋巴母细胞系GM12878的ENCODE染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq）数据，通过UCSC基因组表浏览器中的布罗德（Broad）组蛋白信号强度'StdSig'参数进行处理。