title: GSM1411212: MCF7 Input for MALAT1 CHART-seq; Homo sapiens; OTHER
library_construction_protocol: For CHART-seq, nuclei were isolated from 10^8 MCF-7 cells (ATCC HTB-22) that were crosslinked with 1% formaldehyde for 10 minutes. Nuclei were further crosslinked with 3% formaldehyde for 30 minutes. Chromatin was sheared to a fragment size between 2 kb and 10 kb. Sheared chromatin was incubated overnight with biotinylated DNA oligonucleotides with complementarity to either the NEAT1 or MALAT1 RNAs, and subsequently captured with streptavidin beads. After incubation and washing, captured materials were eluted using RNaseH and subjected to crosslink reversal. DNA was purified by ethanol precipitation and subjected to library construction. Genomic DNA isolated by CHART enrichment, as well as input DNA, was fragmented using sonication. Sonicated DNA was then subjected to end-repair, A-tailing, ligation to universal adapters, amplification with indexed primers, and size selection using SPRI beads.
attributes.tag: GEO Accession
attributes.value: GSM1411212