GSM5388409: CD34+ HSPC replicate 1, C1 capture; Homo sapiens; OTHER
Samples were prepared using the NG Capture-C protocol from Davies, J.O. et al. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat Methods 13, 74-80 (2016), with the following modifications: (1) Five to ten million cells were harvested per sample and the DpnII digestion reactions were scaled down accordingly. (2) DNA was sheared to 200 bp fragments using a Branson 450 Digital Sonifier (Marshall Scientific) (time 18 s, amplitude 20%, pulse 0.5 s, pause 1.5 s; repeat 5x). (3) All of the material from the first capture was used as input for the second round of oligonucleotide capture. (4) Two biological replicates were prepared per sample and pooled for the oligonucleotide capture steps (multliplexed library capture). Illumina sequencing libraries were prepared using the NEBNext DNA Library Prep Reagent Set (E6040S/L). The libraries were sequenced by Novogene Company, Ltd. on an Illumina NovaSeq platform (150 bp paired-end reads).