title: GSM2418376: Hi-C ThymoDp(A)/p(A); Mus musculus; Hi-C
library_construction_protocol: Harvested cells were stained with lineage marker, CD25, CD117, ghost dye red 780. Cells were fixed with PBS containing 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Lineage negative DN2 cells were sorted by FACS AriaII and washed with PBS. Fixed cells were stored at -80 degrees until use. We used in-situ Hi-C to generate a genome-wide contact map essentially as described (Rao, S. S. et al. Cell 159, 1665-1680 2014). Five million cells each of wild-type DN2 and ThymoD-/- DN2 cells were generated using OP9-DL1 stromal cells. Nuclei were resuspended in 0.5% SDS diluted in a final concentration of 1X NEB Buffer 2. Each sequencing library was incubated with USER enzyme for 15 minutes at 37oC after step 56. Final libraries were submitted to paired-end sequencing of 100 bp length on an Illumina HiSeq 2500.
attributes.tag: GEO Accession
attributes.value: GSM2418376