TF ChIP-seq This composite track displays transcription factor (TF) ChIP-seq data from mouse 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 TAL1, GATA1, GATA2, KLF1, NFE2, CTCF, EP300, POL2 (RNA Polymerase II), SA1 (cohesin subunit), SMAD1, BCL11A, ZBTB7A, and many others. Cell types and cell lines represented include G1E, G1E-ER4 (with and without estradiol treatment), MEL (murine erythroleukemia), iMEL (induced MEL), HPC7 (hematopoietic progenitor cells), erythroblasts (ERY), megakaryocytes (MK), and primary blood cell types.
This composite track contains two views:
Tracks can be filtered by cell type, transcription factor, replicate, cell cycle phase, erythroid maturation series, and acute degradation series using the multi-dimensional track configuration matrix.
The G1E cells are an immortalized, GATA1-null cell line derived from mouse embryonic stem cells by gene targeting; these cells proliferate in culture as immature erythroid progenitor cells (Weiss, Yu, Orkin 1997). A stable subline of these cells, called G1E-ER4, undergoes terminal erythroid maturation when GATA1 function is restored as an activatable fusion of GATA1 to the ligand-binding domain of the estrogen receptor (ER). Treatment with estradiol (E2) activates the hybrid protein, allowing synchronous erythroid differentiation and maturation (Gregory et al. 1999). HPC7 cells are an immortalized line that serves as a model for mouse hematopoietic progenitor cells (Pinto do O 2002).
ChIP-seq data were generated in the laboratories contributing to the VISION project and processed through a uniform analysis pipeline. Signal tracks and peak calls were generated using standard ChIP-seq analysis methods. Details of specific datasets and experimental conditions are provided in the metadata for each subtracks.
The data downloads, processing, generation of the tracks displayed, and development of the track hub were done by Belinda Giardine.
Gregory T, Yu C, Ma A, Orkin SH, Blobel GA, Weiss MJ. GATA-1 and erythropoietin cooperate to promote erythroid cell survival by regulating bcl-xL expression. Blood. 1999; 94:87-96. PMID: 10381501.
Pinto do O P, Richter K, Carlsson L. Hematopoietic progenitor/stem cells immortalized by Lhx2 generate functional hematopoietic cells in vivo. Blood. 2002 Jun 1;99(11):3939-46. doi: 10.1182/blood.v99.11.3939. PMID: 12010792.
Weiss MJ, Yu C, Orkin SH. Erythroid-cell-specific properties of transcription factor GATA-1 revealed by phenotypic rescue of a gene-targeted cell line. Mol Cell Biol. 1997; 17:1642-1651. PMID: 9032291; PMCID: PMC231889.
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