GSM4815404: GM12878-SMC1A-ChIA-Drop-Rep1; Homo sapiens; OTHER
The overall chromatin sample preparation for ChIA-Drop is very similar to Hi-C, except without the proximity ligation step in ChIA-Drop.  Similarly, CTCF, cohesin, and RNAPII ChIA-Drop chromatin samples are prepared as they are for respective ChIA-PET experiments but omitting proximity ligation step. Fragmented chromatin sample was mixed with BSA to prevent chromatin aggregation. About 0.5ng of chromatin DNA material was loaded to microfluidics device, Chromium Controller with reagents from Chromium Genome v2 Library Kit & Gel Bead Kit for partitioning of single chromatin complex into individual droplets with unique gel beads according to the manufacturer's protocol with modification. The barcoded DNA amplicons of each chromatin complex were released from all droplets.The purified DNA fragments were subjected for end repair, A-tailing, adaptor ligation, Sample Index PCR and size selection.  The final ChIA-Drop library was sequenced (2× 150 bp) by NextSeq, HiSeq, or NovaSeq runs. We applied microfluidics-based strategy for genome-wide analysis of multiplex chromatin interactions with single-molecule precision (ChIA-Drop). Here, individual chromatin complexes are isolated in droplets that contain a gel bead with unique DNA barcode, in which tethered chromatin DNA fragments are barcoded and amplified for sequencing and mapping to demarcate chromatin contacts.
GEO
GSM4815404