ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR364/SRR364999/SRR364999_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR365/SRR365000/SRR365000_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR365/SRR365001/SRR365001_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR364/SRR364997/SRR364997.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR364/SRR364999/SRR364999_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR365/SRR365000/SRR365000_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR364/SRR364998/SRR364998_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR365/SRR365001/SRR365001_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR364/SRR364998/SRR364998_1.fastq.gzprimaryOK200GenomicsMolecular Biology, MGHhttps://www.ebi.ac.uk/ena/browser/view/PRJNA139533Drosophila melanogasterxref:PubMed:22143764Long non-coding RNAs (lncRNAs) have important regulatory roles and can function at the level of chromatin. To determine where lncRNAs bind to chromatin, we developed CHART, a hybridization-based technique that specifically enriches endogenous RNAs along with their targets from reversibly-crosslinked chromatin extracts. CHART was used to enrich the DNA and protein targets of endogenous lncRNAs from fly and human. This analysis was extended to genome-wide mapping of roX2, a well-studied ncRNA involved in dosage-compensation in Drosophila. CHART revealed that roX2 binds at specific genomic sites that coincide with the binding sites of proteins from the MSL-complex that affects dosage compensation. These results reveal the genomic targets of roX2 and demonstrate how CHART can be used to study RNAs in a manner analogous to ChIP for proteins. Overall design: Examination of the binding sites of roX2 ncRNA from S2 cells using two different elution strategies compared with a sense control or input control. Processed data file 'roX2.2.peaks.bed' (for roX2 CHART RNase eluted, combined replicates) linked below as supplementary file.ENAfalseDrosophila melanogasterThe Genomic Binding Sites of an Endogenous Non-Coding RNA2025-09-242013-05-31PRJNA139533GSE28180722722143764