• Protocols

  • Resources

We curated a repository of datasets and analysis resources that can be used to support investigators as they pursue research endeavors in benign hematology.
While our list is expanding, current resources feature:

Single cell RNA-sequencing of mouse hematopoietic cells isolated from the hemogenic endothelium

  1. DESIGN: Single cell RNA-sequencing (10X Genomics platform) of murine E9-9.5 P-Sp/AGM-derived FACS-isolated VE-Cadherin+CD61+EPCR+ cells
  2. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171457
  3. PubMed: https://pubmed.ncbi.nlm.nih.gov/34525376/
  4. GitHub: https://github.com/FredHutch/dignum-etal-2021

Single cell RNA-sequencing of a) AGM-derived cells transitioning from hemogenic endothelium to hematopoietic stem cels and b) AGM-derived endothelial cells

  1. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145886
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/35332125/
  3. GitHub: https://github.com/FredHutch/hadland-etal-2022
  4. DESIGN: Single cell RNA-sequencing (10X Genomics platform) of murine E10-E11 AGM-derived cultured endothelial cells expressing mAkt (AGM-EC) used as stroma to support HSC development ex vivo; and murine E10-E11 AGM-derived FACS-isolated VE-Cadherin+CD61+EPCR+ cells enriched for HSC precursors (primary cells and progeny following co-culture with AGM-EC)

Single cell RNA-sequencing of mouse fetal liver-derived endothelial cells and mouse fetal liver-isolated hematopoietic stem cells

  1. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233031
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/40971295/
  3. GitHub: https://github.com/FredHutch/Ishida-etal-2023
  4. DESIGN: single cell RNA-sequencing (10X Genomics platform) of murine E12 FL-derived cultured endothelial cells expressing mAkt (FL-EC) used as stroma to support HSC development/expansion ex vivo; and murine E13.5 FL-derived FACS-isolated VEcadherin-/low,CD45+,Gra1-F4/80-,Sca1+,EPCR+ cells enriched for HSCs (primary cells and progeny following co-culture with FL-EC). Sample 4 also included CD11b-ESAM expression in sorting.

Human umbilical vein endothelial cells (HUVECs) cultured under various levels of hydrostatic pressure with flow

  1. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE261063
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/41378902/
  3. GitHub: https://github.com/FredHutch/Mandrycky-etal-2024
  4. DESIGN: single cell RNA-sequencing (10X Genomics platform) of HUVECs cultured in microfluidic vessels and subjected to various levels of hydrostatic pressure (0, 20 and 60 mmHg), while maintained under constant shear stress (flow). A static sample was also included as a negative control.

Single cell RNA-sequencing of human induced pluripotent stem cell-derived embryoid bodies during hematopoietic differentiation

  1. https://cellxgene.cziscience.com/collections/4a2c25af-558a-45fc-bc9a-54ec44a1d63f
  2. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE274082 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE274084
  3. GitHub: https://github.com/FredHutch/Wellington-et-al-2024
  4. DESIGN: Single-cell combinatorial indexing RNA-seq (sci-RNA-seq) of human iPSC-derived embryoid bodies spanning day 7 through day 21 of hematopoietic differentiation. 10X 3’ sc-RNA-seq of human iPSC-derived embryoid bodies from day 8 of differentiation integrated with 10X 3’ sc-RNA-seq published human embryo datasets encompassing HSC-independent , Carnegie Stage (CS) 10-13 (Zeng et al. 2019), and HSC-dependent, CS 14-17 (Crosse et al. 2020, Calvanese et al. 2022), timepoints. There are 3 visualizations: (1) sci-RNA-seq Days 7-21 iPSC-derived Embryoid Bodies during Hematopoietic Differentiation, (2) 10X Day 8 iPSC-derived Embryoid Body during Hematopoietic Differentiation data alone, and (3) 10X Day 8 iPSC-derived Embryoid Body during Hematopoietic Differentiation integrated with human embryo 10X data from Zeng et al. 2019, Crosse et al. 2020, and Calvanese et al. 2022.

Single-cell RNA-sequencing of mouse hematopoietic stem cells and multipotent progenitor cells and accompanied whole-genome bisulfate sequencing of hematopoietic stem cells

  1. https://www.ebi.ac.uk/biostudies/ArrayExpress/studies/E-MTAB-2262?query=E-MTAB-2262
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/25158935/
  3. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52709
  4. Unimported: https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-GEOD-52709
  5. DESIGN: Global transcriptome analysis of of ex vivo isolated mouse multipotent hematopoietic stem cells (HSC) and multipotent progenitor cells (MPP1-MPP4) as revealed by next-generation sequencing (RNA-seq) ; whole-genome bisulfite sequencing of hematopoietic stem cells (HSCs) and 3 different multipotent progenitor subpopulations (MPP). Three independent biological replicates each were analyzed.

Single-cell RNA-sequencing of mouse hematopoietic stem cells and GMPs upon TNFα treatment ex vivo or in vivo

  1. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115403
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/31230859/
  3. DESIGN: RNA sequencing of 3 biological replicates of HSCs (Lin-/cKit+/Sca1+/Flk2-/CD48-/CD150+) and GMPs (Lin-/cKit+/Sca1-/FcγR+/CD34+) treated ± TNFα both ex vivo for 3 and 12 hours and in vivo for 3 hour (1x3hr). For ex vivo treatment of TNFα, HSCs and GMPs were isolated by FACS from C57BL/6 mouse bone marrow (BM) and cultured in liquid media ± TNFα for either 3 or 12 hours. For in vivo treatment, HSCs and GMPs were isolated from C57BL/6 mice 3 hours after a single injection of PBS or TNFα.

Bulk RNA-seq of Young and Aged hematopoietic cells

  1. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162607
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/35577813/
  3. Design: Purified HSCs, multipotent progenitor (MPP) 1, megakaryocyte/erythroid-biased MPP2, myeloid-biased MPP3, lymphoid-primed MPP4, granulocyte-macrophage progenitors (GMPs), megakaryocyte-erythrocyte progenitors (MEPs), and common lymphoid progenitors (CLPs) from 10-week-old (Young) and 20-month-old aged (Aged) mice

Bulk RNA sequencing of human megakaryocyte-erythroid progenitor (MEP) cells

  1. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112692
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/30463007/
  3. Design: bulk RNAseq of primary human CMP, ErP, MkP, and MEP sorted from mobilized peripheral blood
  4. Visualizer: https://altanalyze.org/ICGS/MEP/index.php

Single-cell RNA sequencing of mouse bone marrow stroma

  1. Raw data: https://osf.io/ne9vj
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/33777933/
  3. Design: Mouse adult bone marrow stromal cells
  4. Visualizer: https://singlecell.broadinstitute.org/single_cell/study/SCP1248/resolving-the-bone-marrow-niche-heterogeneity#study-visualize

CITE-seq analysis of human bone marrow

  1. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245108
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/38514887/
  3. Design: Fresh bone marrow aspirates from human donors analyzed using CITE seq
  4. Visualizer: https://altanalyze.org/MarrowAtlas/

The Human Cell Atlas bone marrow single-cell interactive web portal

  1. PubMed: https://pubmed.ncbi.nlm.nih.gov/30243574/
  2. Design: Bone marrow small conditional RNA-sequencing data from eight healthy human donors
  3. Visualizer: https://www.altanalyze.org/ICGS/HCA/splash.php

Temporal expression profile of human megakaryocytic differentiation from primary CD34+ cells

  1. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/17309828/
  3. Design: microarray RNA expression from primary human CD34 cells differentiated to megakaryocytes in vitro

Single cell RNA-sequencing of mouse hematopoietic cells isolated from the hemogenic endothelium

  1. DESIGN: Single cell RNA-sequencing (10X Genomics platform) of murine E9-9.5 P-Sp/AGM-derived FACS-isolated VE-Cadherin+CD61+EPCR+ cells
  2. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171457
  3. PubMed: https://pubmed.ncbi.nlm.nih.gov/34525376/
  4. GitHub: https://github.com/FredHutch/dignum-etal-2021

Single cell RNA-sequencing of a) AGM-derived cells transitioning from hemogenic endothelium to hematopoietic stem cels and b) AGM-derived endothelial cells

  1. GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145886
  2. PubMed: https://pubmed.ncbi.nlm.nih.gov/35332125/
  3. GitHub: https://github.com/FredHutch/hadland-etal-2022
  4. DESIGN: Single cell RNA-sequencing (10X Genomics platform) of murine E10-E11 AGM-derived cultured endothelial cells expressing mAkt (AGM-EC) used as stroma to support HSC development ex vivo; and murine E10-E11 AGM-derived FACS-isolated VE-Cadherin+CD61+EPCR+ cells enriched for HSC precursors (primary cells and progeny following co-culture with AGM-EC)
  1. Whole cell proteome analysis of FACS-sorted mouse hematopoietic stem cells and multipotent progenitor cells
    1. DESIGN: Whole cell proteome analysis of FACS-sorted mouse HSCs and MPP1
    2. Proteome Central: https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000572
    3. PubMed: https://pubmed.ncbi.nlm.nih.gov/25158935/
  2. Mass spectrometry analysis of aged and adult mouse hematopoietic stem cells, multipotent progenitors, and oligopotent progenitors
    1. DESIGN: Mouse hematopoietic cells from bone marrow of young (8-14 weeks) or old (24-27 months) C57Bl/6 mice.
    2. ProteomeCentral: https://proteomecentral.proteomexchange.org/ui?pxid=PXD017442
    3. PubMed: https://pubmed.ncbi.nlm.nih.gov/33236985/
  1. Microarray data from many (~50) hematopoietic types mostly from Irv Weissman’s lab: https://gexc.riken.jp/
  2. The Dependency Map (DepMap): https://depmap.org/portal/
  3. The Cell Marker Accordion Code: https://github.com/TebaldiLab/cellmarkeraccordion
  4. AltAnalyze Comprehensive Analysis Code: https://altanalyze.org/
  5. Alt Analyze Stromal Single Cell Browser: https://altanalyze.org/ICGS/Public/Scadden-Stromal/User.php
  6. Tabula Muris – Single Cell Transcriptome of Mus Musculus: https://tabula-muris.sf.czbiohub.org/

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