Description

TF ChIP-seq
This composite track displays transcription factor (TF) ChIP-seq data from human hematopoietic cell types as part of the VISION project (ValIdated Systematic IntegratiON of hematopoietic epigenomes). The tracks provide genome-wide maps of transcription factor binding sites determined by chromatin immunoprecipitation followed by sequencing (ChIP-seq).

The transcription factors profiled include BCL11A, CTCF, EP300, GATA1, GATA2, KLF1, NFE2, POL2 (RNA Polymerase II), SA1 (cohesin subunit), SMAD1, TAL1, and ZBTB7A. Cell types represented include erythroblasts (ERY), neutrophils (NEU), K562 cells, and HUDEP-2 cells (including BCL11A-ER-V5 expressing and Delta-Ggamma variants).

Display Conventions and Configuration

This composite track contains three views:

Signal

The ChIP-seq signal track, displayed as a continuous variable along the chromosomes.

Fold-change

The fold-change of ChIP-seq signal over input control.

Peaks

The called peaks representing transcription factor binding sites.

Tracks can be filtered by cell type, transcription factor, and replicate using the track configuration matrix.

Methods

ChIP-seq data were downloaded from published sources and processed through the VISION data pipeline. Signal tracks, fold-change over control, and peak calls were generated using standard ChIP-seq analysis methods. CUT&RUN data for KLF1 in CD34+ cells differentiated to orthochromatic erythroblasts are also included.

Credits

The data downloads, processing, generation of the tracks displayed, and development of the track hub were done by Belinda Giardine.

References

Heuston EF, Keller CA, Lichtenberg J, Giardine B, Anderson SM; NIH Intramural Sequencing Center; Hardison RC, Bodine DM. Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points. Epigenetics Chromatin. 2018 May 28;11(1):22. PMID: 29807547; PMCID: PMC5971425.

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.

Data Release Policy

These data are available for use without restrictions.

Contact

Ross Hardison rch8@psu.edu