These tracks show the signals and estimated expression levels for RNA-seq of total RNA from several hematopoietic cell types in adult mice plus the cell line system G1E and G1E-ER4. The Scriptseq method was used, which results in directional data (distinguishing RNA from the two strands of DNA). The sequencing method generated paired-end reads.
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 minus strand, and negative values are used in the display. The Expression track displays a summary of the gene expression level in each cell type by different colors for an icon covering each gene. In those colors, blue denotes low level expression, whereas red is a high level.
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.
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).
The Scriptseq method was used to prepare the libraries for sequencing. Details of the procedure and data analysis are described in Heuston et al. (2018), and Xiang et al. (2020).
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.
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, Keller CA, Heuston E, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, Taylor J, Blobel GA, Weiss MJ, Cheng Y, Yue F, Hughes J, Higgs DR, Zhang Y, Hardison RC. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome Res. 2020 Mar;30(3):472-484. PMID: 32132109; PMCID: PMC7111515.
These data are available for use without restrictions.
Ross Hardison rch8@psu.edu