GSM1420138: Hi-C clone8 Wild type 1; Drosophila melanogaster; OTHER
Hi-C in S2 or clone8 cells was carried out as described (Belton et al., 2012) with a few modifications to account for Drosophila cell and genome size: 50 million fixed insect cells per sample were used and batches of 20 million cells each were digested with 400U HindIII as Hi-C samples with a control 3C sample of 10 million cells. Cohesive ends in Hi-C samples were filled in with dATP, dGTP, dTTP and biotin-14-dCTP. Then DNA was ligated, purified and sonicated. Size selection for ~230bp fragments carried out and then enriched for biotinylated specimen with straptavidin beads. Illumina paired-end adapters and PfuUltra II Fusion DNA polymerase were used for S2 library generation while TruSeq adapters and Q5 DNA polymerase were used for clone8 samples. For all libraries 10 cycles of PCR amplification were used. 50 million S2 cells were collected and resuspended in 22.5ml of fresh medium. Clone8 cells were washed with PBS and 22.5ml of fresh medium added. 37% formaldehyde solution was added to obtain a final concetration of 1%, followed by incubation at room temperature for 10min. 1.25ml 2.5M glycine solution was added and incubated for another 5 min at RT followed by 10min on ice.
GEO Accession
GSM1420138