Table 2.
Recent System-wide Epigenetic Datasets for Inferring Regulatory Networks of Hematopoiesis
| Description | Reference | Accession | ||
|---|---|---|---|---|
| Chromatin accessibility | Mus musculus | Spatial genome re-organization between fetal and adult hematopoietic stem cells (ATAC-seq). | Chen et al. (2019) | GSE119198 |
| Homo sapiens | ATAC-seq profiles of hematopoietic and leukemic cell types, across 13 normal hematopoietic cell types and three acute myeloid leukemia cell types. The complete dataset contains a total of 132 samples. | Corces et al. (2016) | GSE74912 | |
| Single-cell ATAC-seq (scATAC-seq) of lymphoid-primed multipotential progenitors, monocytes, leukemic stem cells, and leukemic blast cells. | Corces et al. (2016) | GSE74310 | ||
| Single-cell epigenomics and transcriptomics mapping the continuous regulatory landscape of 10 cell types of human hematopoietic differentiation (bulk and single-cell ATAC-seq). | Buenrostro et al. (2018) |
GSE96769, GSE96771 |
||
| Integrated epigenomic and transcriptomic profiling of terminal human erythropoiesis (bulk ATAC-seq). | Ludwig et al., 2019 | GSE115672 | ||
| ChIP-seq | Mus musculus | ChIP-seq of granulocyte-monocyte progenitor cells | Olsson et al., 2016 | GSE70237 |
| Chromatin state dynamics during blood formation. The iChIP method was used to profile the chromatin dynamics during hematopoiesis across 16 different cell types, which include the principal hematopoietic progenitors. | Lara-Astiaso et al. (2014) | GSE59636 | ||
| ChIP-seq of Lin−CD34+ and Lin−CD34− cells. | You et al., 2018 | GSE100689 | ||
| Spatial genome re-organization between fetal and adult hematopoietic stem cells (ChIP-seq). | Chen et al. (2019) | GSE119200 | ||
| Methylation | Mus musculus | The complete methylome of hematopoietic stem cells and their immediate progeny. Whole-genome bisulfite sequencing was performed on hematopoietic stem cells and their immediate progeny, namely, three different multipotent progenitor subpopulations (MPP, MPP1, and MPP2). | Cabezas-Wallscheid et al. (2014) | GSE52709 |
Systemic epigenetic profiling of mouse and human hematopoietic populations using ATAC-seq, ChIP-seq, and whole-genome bisulfite sequencing was collected from the literature and sorted into the table. The accession numbers from NCBI GEO were also listed. The datasets were found by searching the keywords “hematopoiesis” and “ATAC” or “ChIP” or “bisulfite” in NCBI GEO datasets portal uploaded in the previous 6 years and manually refined.