These tracks show the signals for RNA-seq of polyA+ RNA from several hematopoietic cell types in adult mice plus the cell line system G1E and G1E-ER4. The polyA+ fraction of RNA was isolated prior to making the libraries for RNA-seq.
One set of samples focused on the megakaryocyte-erythroid progenitor cell population (MEP, isolated from adult mouse bone marrow) and representatives of cell types derived from it, megakaryocytes and erythroblasts isolated from mouse fetal liver. These data are directional (distinguishing the two strands) and used paired-end sequencing.
PolyA+ RNA-seq was also determined as a time course of differentiation and maturation of G1E-ER4 cells in response to activation of function of the transcription factor GATA1. Most of these data are also directional and used paired-end sequencing. Additional data sets in this system generated non-directional data. Data are also included for the cell lines MEL and CH12.
For directional data, two RNA-seq signal tracks are provided for each replicate in each cell type. Coverage plus strand shows the signal strength for RNA synonymous with the top or plus strand, and positive values are used in the display. Coverage minus strand shows the signal strength for RNA synonymous with the bottom or minu strand, and negative values are used in the display. For data that is non-directional, the signal tracks can be viewed as Coverage unstranded.
The track names give an abbreviation for the blood cell type or cell line. Biological replicates are distinguished by a VISION sample id, a 3- or 4-digit number, at the beginning of the track name.
Mouse primary blood cells purified predominantly using cell surface markers include: LSK = Lin-Sca1+Kit+ cells from mouse bone marrow containing hematopoietic stem and progenitor cells, CMP = common myeloid progenitor cell, MEP = megakaryocyte-erythrocyte progenitor cell, ERY = erythroblast, GMP = granulocyte monocyte progenitor cell, MON = monocyte, NEU = neutrophil, CFUE = colony forming unit erythroid, CFUMK = colony forming unit megakaryocyte, MK = megakaryo = megakaryocyte.
Data from several immortalized cell lines were included. 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). Untreated G1E-ER4 cells, carrying the inactive GATA1-ER, proliferate without differentiation, but treatment with estradiol (E2) activates the hybrid protein, effectively complementing the GATA1 loss-of-function and allowing synchronous erythroid differentiation and maturation (Gregory et al. 1999). An additional cell line model used here are murine erythroleukemia (MEL) cells, which can be chemically induced to mature into erythroblast-like cells with increased hemoglobin (iMEL). CH12 cells are an immortalized line that is a model for mouse B cells; the epigenetic data on CH12 cells were used to generate the B cell epigenetic state annotation.
Details of the procedure and data analysis are described in Jain et al. (2015), Mishra et al. (2025), and Paralkar et al. (2016).
Belinda Giardine generated the tracks displayed and developed the track hub.
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.
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.
Jain D, Mishra T, Giardine BM, Keller CA, Morrissey CS, Magargee S, Dorman CM, Long M, Weiss MJ, Hardison RC. Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system. Genom Data. 2015 Jun 1;4:1-7. doi: 10
Mishra T, Giardine BM, Morrissey CS, Keller CA, Heuston EF, Anderson SM, Paralkar VR, Pimkin M, Weiss MJ, Bodine DM, Hardison RC. Divergence between transcriptomes and chromatin accessibility during differentiation from a bipotential progenitor cell population to erythroblasts and megakaryocytes. bioRxiv [Preprint]. 2025 Jul 3:2025.06.30.662383. doi: 10.1101/2025.06.30.662383. PMID: 40631103; PMCID: PMC12236744.
Paralkar VR, Taborda CC, Huang P, Yao Y, Kossenkov AV, Prasad R, Luan J, Davies JO, Hughes JR, Hardison RC, Blobel GA, Weiss MJ. Unlinking an lncRNA from Its Associated cis Element. Mol Cell. 2016 Apr 7;62(1):104-10. doi: 10.1016/j.molcel.2016.02.029. Epub 2016 Mar 31. PMID: 27041223; PMCID: PMC4877494.
These data are available for use without restrictions.
Ross Hardison rch8@psu.edu