Sonication series for ChIP-seq This composite track displays ChIP-seq data from a systematic evaluation of sonication conditions for chromatin immunoprecipitation in G1E-ER4 cells treated with estradiol. The experiment tested the effect of varying the number of sonication cycles (3, 4, 5, 7, 10, and 15 cycles) and the number of input cells (1 million, 5 million, 20 million, and 50 million) on ChIP-seq signal quality and peak calling for the transcription factors TAL1 and CTCF.
These data allow assessment of how sonication parameters affect the reproducibility and sensitivity of ChIP-seq experiments in hematopoietic cells, and can guide optimization of ChIP-seq protocols.
This composite track contains two views:
Tracks can be filtered by antibody (TAL1 or CTCF). The track names include the VISION sample id, the antibody target, cell type, number of sonication cycles, and number of input cells.
ChIP-seq was performed on G1E-ER4 cells treated with estradiol to activate GATA1-ER, using antibodies against TAL1 and CTCF. Chromatin was sonicated with varying numbers of cycles and varying amounts of input cells. Libraries were sequenced, mapped, and processed to generate signal and peak tracks.
Belinda Giardine generated the tracks displayed and developed the track hub.
Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria MEG, Schatz MC, Taylor J, Göttgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome Res. 2024 Aug 20;34(7):1089-1105. PMID: 38951027; PMCID: PMC11368181.
These data are available for use without restrictions.
Ross Hardison rch8@psu.edu