ChIP-Atlas: SRX4053977

Antigen

Cell type Class: Pluripotent stem cell
Cell type: Embryoid Bodies
MeSH Description: Spontaneous aggregations of human embryonic stem cells that occur in vitro after culturing in a medium that lacks LEUKEMIC INHIBITORY FACTOR. The embryoid bodies can further differentiate into cells that represent different lineages.

library_strategy: ATAC-seq
library_source: GENOMIC
library_selection: other
library_construction_protocol: ATAC-seq: 50.000 cells were harvested and washed twice in cold 1X PBS. Cells were resuspended in 10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, and 0.1% NP-40 and centrifuged immediately at 4°C. The pellet was resuspended in 25 ul of 2x TD buffer, 2.5 ul TDE1 (Nextera DNA sample preparation kit, FC-121-1030) followed by incubation for 30 min at 37C. The reaction was then cleaned by Min-elute PCR purification kit (Qiagen, 28004). The optimal number of PCR cycles were determined to be the 1/3 of the maximum fluorescence measured by qPCR reaction with 1X SYBR Green (Invitrogen), custom designed primers (Buenrostro et al., 2013) and 2X NEB MasterMix (New England Labs, M0541). Following PCR enrichment, the library was cleaned with min-elute PCR kit and quantified using Qubit (Life Technologies, Q32854). Nextera DNA sample preparation kit, FC-121-1030 was used for ATAC-seq. The fragment length distribution of the library was determined by Agilent High Sensitivity DNA D1000 Screentape (5067- 5585) system and the final quantification of the library before pooling was done with KAPA library amplification kit (Roche Lightcycler 480).