EXPERIMENT_TITLE: GSM3611748: GM17879 Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Lymphocytes were isolated from whole blood samples by centrifugation after dilution with PBS and underlaying Sigma Histopaque-1077 to the bottom. Genomic DNA and total RNA were extracted simultaneously from lymphocytes using QIAGEN's AllPrep DNA/RNA Mini Kit. Five million cells were crosslinked with formaldehyde and lysed with protease inhibitors (Sigma, P8340). Chromatins were subsequently digested by MboI restriction enzyme (NEB, R0147). Restriction fragment overhangs were filled and the DNA ends were marked with biotin. Next, biotinylated DNA were sheared to a size of 300-500 bp, whose ends were repaired subsequently. dATP were attached and Illumina indexed adapter (TrueSeq nano) were ligated. The DNA fragments were then amplified and purified.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Background: In both Turner syndrome (TS) and Klinefelter syndrome (KS) copy number aberrations of the X chromosome lead to various developmental symptoms. To date there has not been a comprehensive and directly comparative analysis of TS vs. KS regarding the changes on the molecular level Methods: We analyzed gene expression patterns with RNA-Seq and DNA methylation patterns with the CpGiant assay in lymphocytes, and chromatin conformation with in situ Hi-C in lymphoblastoid cell lines, from TS and KS patients together with their same gender controls. Results: In TS, differentially expressed escape genes were downregulated but differentially expressed inactive genes were upregulated. In KS, differentially expressed escape genes were upregulated while inactive genes appeared unchanged. Interestingly, 81 differentially expressed genes (DEGs) were associated with both TS and KS, and uniformly displayed expression changes into opposite directions. DEGs on the X chromosome and the autosomes were coexpressed in both TS and KS, indicating that there are molecular ripple effects of the changes in X chromosome dosage that extend to autosomes. Four potentially candidate genes (RPS4X, SEPT6, NKRF and CX0rf57) for KS were identified on Xq. Broad hypomethylation of the X chromosome is observed in TS whereas hypermethylation of chromosome X is present in KS. Only promoters of inactive genes were differentially methylated in both TS and KS while escape genes remained unchanged. The intrachromosomal contact map of the X chromosome in TS was partitioned into two superdomains and exhibited the structure of an active X chromosome. Conclusions: Components of the molecular basis of TS and KS were identified on the levels of the transcriptome and the epigenome, with candidate central genes on Xp for TS and on Xq for KS. The discovery of shared DEGs indicates the existence of common molecular mechanisms for gene regulation in TS and KS that are transmitting the gene dosage changes to the transcriptome. Overall design: A direct comparative analysis of TS versus KS and integrative analysis over three levels of genomic and functional genomic activity, in primary lymphocytes from patients and controls for levels of gene expression and levels of DNA methylation and in LCLs for chromosome folding patterns
SAMPLE_TITLE: GM17879 Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "lymphoblastoid cell"}, {"TAG": "biomaterial_provider", "VALUE": "Coriell; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM17879"}, {"TAG": "chromosomes", "VALUE": "XXY"}, {"TAG": "cell line", "VALUE": "GM17879"}, {"TAG": "cell type", "VALUE": "lymphoblastoid cell"}]
Pool_Member_@attributes_sample_title: GM17879 Hi-C
RUN_SET_RUN_Pool_Member_@attributes_sample_title: GM17879 Hi-C
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8588405.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR008/588/SRR8588405.sralite.1", "size": "24059627475", "date": "2020-06-23 15:03:52", "md5": "87888ada7493a354bce3e9646aaf2a63", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8588405", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8588405/SRR8588405", "size": "41878914715", "date": "2019-02-19 00:17:02", "md5": "651aff3a25588812ca50a183d68d8e08", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "KS-TGACCA_S1_L008_R2_001.fastq.gz", "size": "32023397243", "date": "2020-03-10 14:00:24", "md5": "548a262a0f3d99760471f6ee0fc3ae84", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "KS-TGACCA_S1_L008_R1_001.fastq.gz", "size": "28305434597", "date": "2020-03-10 15:39:45", "md5": "f97dbc016121de72186584c13d65a36b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]