title: GSM4873514: org_fetal_rep2_hic; Mus musculus; Hi-C
library_construction_protocol: Fetal spheroids and adult organoids corresponding to approximately one million cells per replicate were released from Matrigel and fragmented by repeated washing with cold PBS with 0.1% BSA. The organoid fragments were cross-linked in 2% formaldehyde for 20 minutes, quenched, and washed. Following, the cells were lysed and chromatin was digested with 2 units of DNase I for 5 minutes. The nuclei were purified with AMPure XP beads and washed followed by end repair and dA-tailing reactions. Biotin-labeled bridge adapters were then ligated overnight to the fragments followed by another round of purification with AMPure XP beads and washing. The nuclei were treated with PNK to phosphorylate adapters and ligation prior to reversal of cross-linking, DNA precipitation and purification. The ligation products with biotin were then pulled down with MyOne C1 beads followed by washing and end repair, dA-tailing, and ligation of sequencing adapters. The libraries were amplified for 14 PCR cycles with primers containing Nextera barcodes for sample multiplexing: N701 (TCGCCTTA), N702 (CTAGTACG), N703 (TTCTGCCT), and N704 (GCTCAGGA). Libraries were then purified and quantified with Qubit and Fragment Analyzer (Agilent) and the four libraries were pooled and paired-end sequenced with Illumina NextSeq.
attributes.tag: GEO Accession
attributes.value: GSM4873514