Table 1.
Recent System-wide Gene Expression Datasets for Inferring Transcription Regulatory Networks of Hematopoiesis
| Description | Reference | Accession | ||
|---|---|---|---|---|
| Gene expression | Mus musculus | Immunological Genome Project gene expression profiling for 103 different immunocytes by RNA-seq. Immune cell populations were isolated with high purity by flow cytometry. | Yoshida et al. (2019) | GSE109125 |
| Total RNA was obtained from 54 hematopoietic cells types and eight non-hematopoietic out-groups for microarray. | de Graaf et al., 2016 | GSE77098 | ||
| Comparison of gene expression in different hematopoietic cell types (RNA-seq). | Choi et al., 2019 | GSE116177 | ||
| Transcriptional heterogeneity and lineage commitment in myeloid progenitors (scRNA-seq). | Paul et al. (2015) | GSE72857 | ||
| Transcriptional plasticity, priming, and commitment in hematopoietic lineages. Bone marrow hematopoietic progenitor mRNA profiles from single cells were generated by deep sequencing of thousands of single cells (scRNA-seq). | Giladi et al. (2018) | GSE92575 | ||
| The transcriptional landscape of mouse blood stem/progenitor cell transitions at single-cell resolution (scRNA-seq). | Nestorowa et al., 2016 | GSE81682 | ||
| Gene expression in hematopoietic stem and progenitor cells from Gata1-EGFP reporter mouse bone marrow (microarray). | Drissen et al., 2016 | GSE49241 | ||
| Distinct myeloid progenitor differentiation pathways uncovered through scRNA-seq. | GSE77029 | |||
| Identification of subset-specific dendritic cell progenitors revealing early commitment in the bone marrow (scRNA-seq). | Schlitzer et al., 2015 | GSE60781 | ||
| scRNA-seq profiling of common myeloid progenitor (CMP) cells. | Olsson et al., 2016 | GSE70236 | ||
| scRNA-seq profiling of hematopoietic progenitors from mouse bone marrow and fetal liver. | Tusi et al., 2018 | GSE89754 | ||
| Homo sapiens | Distinct routes of lineage development reshape the human blood hierarchy across ontogeny. Using SMART-seq, the expression profile of the hematopoietic stem cells and other hematopoietic progenitors (12 samples in duplicates) were analyzed. | Notta et al. (2016) | GSE76234 | |
| scRNA-seq of human hematopoietic stem and progenitors (HSPCs). Lin−CD34+CD38+ progenitors and Lin−CD34+CD38− stem cell-enriched HSPCs were individually sorted, their surface marker fluorescence intensities were recorded, and they were subjected to scRNA-seq. | Velten et al. (2017) | GSE75478 | ||
| Comparison of gene expression in different human hematopoietic cell types (bulk RNA-seq). | Choi et al., 2019 | GSE115736 | ||
| The expression profiles of fetal and adult human erythroblasts at two differentiation stages by bulk RNA-seq. | Huang et al., 2017 | GSE102182 | ||
| mRNA profiles of fetal and adult erythroblasts were generated by bulk RNA-seq. | Lalonde et al., 2017 | GSE90878 | ||
| Transcriptional profiling in human primary fetal and adult CD34+ HSPCs and erythroid progenitor cells by RNA-seq. | Liu et al., 2017 | GSE74053 | ||
| Single-cell epigenomics and transcriptomics mapping the continuous regulatory landscape of 10 cell types of human hematopoietic differentiation (scRNA-seq). | Buenrostro et al. (2018) | GSE96811 | ||
| Transcription profiles of hematopoietic and leukemic cell types assayed using unstranded RNA-seq, across 13 normal hematopoietic cell types and three acute myeloid leukemia cell types. The complete dataset contains a total of 81 samples. | Corces et al. (2016) | GSE74246 | ||
| CD34+-derived erythroblasts grown in in vitro culture were sorted using surface markers and processed using bulk RNA-seq. | Ludwig et al., 2019 | GSE115678 | ||
| Developmental differences between neonatal and adult human erythropoiesis (bulk RNA-seq). | Yan et al., 2018 | GSE107218 | ||
| RNA-seq profiles of eight primary human hematopoietic progenitor populations representing the major myeloid commitment stages and the main lymphoid stages. | Chen et al., 2014 | EGAD00001000745 | ||
Systemic transcriptome profiling of mouse and human hematopoietic populations using microarray, bulk and single-cell (sc) RNA-seq was collected from literatures and sorted into the table. The accession numbers initiated with GSE are from NCBI Gene Expression Omnibus (GEO), whereas the one initiated with EGA is from European Genome-phenome Archive (EGA). The datasets were found by searching the keyword “hematopoiesis” in NCBI GEO and EGA datasets portal uploaded in the previous 6 years, filtered by the RNA sample type and manually refined.