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Home Omics
Knowledge
Human Mouse Zebrafish In vitro
Hematopoietic References
Metadata
Datasets Samples/Cells Cell Types Genes Publications
Featured Functions
Cross-stage analysis Cross-species analysis Cross-model analysis
HSPC Development
HSPC inter-stage heterogeneity Intrinsic regulatory program Extrinsic cell-cell communication
Statistics
Help
FAQ Contact Us
Download
HemAtlas

HemAtlas
Mapping developmental hematopoiesis across stages, species and models

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Publications
1. A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis.
Xue Y, Liu D, Cui G, Ding Y, Ai D, Gao S, Zhang Y, Suo S, Wang X, Lv P, Zhou C, Li Y, Chen X, Peng G, Jing N, Han JJ, Liu F.
Cell reports. 2019-04-01
PMID: 31042481 | DOI: 10.1016/j.celrep.2019.04.030
2. Identification of HSC/MPP expansion units in fetal liver by single-cell spatiotemporal transcriptomics.
Gao S, Shi Q, Zhang Y, Liang G, Kang Z, Huang B, Ma D, Wang L, Jiao J, Fang X, Xu CR, Liu L, Xu X, Göttgens B, Li C, Liu F.
Cell research. 2021-08-02
PMID: 34341490 | DOI: 10.1038/s41422-021-00540-7
3. Multi-layered Spatial Transcriptomics Identify Secretory Factors Promoting Human Hematopoietic Stem Cell Development.
Crosse EI, Gordon-Keylock S, Rybtsov S, Binagui-Casas A, Felchle H, Nnadi NC, Kirschner K, Chandra T, Tamagno S, Webb DJ, Rossi F, Anderson RA, Medvinsky A.
Cell stem cell. 2020-09-17
PMID: 32946788 | DOI: 10.1016/j.stem.2020.08.004
4. Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates.
Ding Y, Wang W, Ma D, Liang G, Kang Z, Xue Y, Zhang Y, Wang L, Heng J, Zhang Y, Liu F.
Blood. 2021-01-01
PMID: 32756943 | DOI: 10.1182/blood.2020005219
5. G protein-coupled receptor 183 facilitates endothelial-to-hematopoietic transition via Notch1 inhibition.
Zhang P, He Q, Chen D, Liu W, Wang L, Zhang C, Ma D, Li W, Liu B, Liu F.
Cell research. 2015-09-11
PMID: 26358189 | DOI: 10.1038/cr.2015.109
6. A single-cell resolution developmental atlas of hematopoietic stem and progenitor cell expansion in zebrafish.
Xia J, Kang Z, Xue Y, Ding Y, Gao S, Zhang Y, Lv P, Wang X, Ma D, Wang L, Han JJ, Liu F.
Proceedings of the National Academy of Sciences of the United States of America. 2021-04-01
PMID: 33785593 | DOI: 10.1073/pnas.2015748118
7. Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing.
Tang Q, Iyer S, Lobbardi R, Moore JC, Chen H, Lareau C, Hebert C, Shaw ML, Neftel C, Suva ML, Ceol CJ, Bernards A, Aryee M, Pinello L, Drummond IA, Langenau DM.
The Journal of experimental medicine. 2017-09-06
PMID: 28878000 | DOI: 10.1084/jem.20170976
8. The transcriptional landscape of hematopoietic stem cell ontogeny.
McKinney-Freeman S, Cahan P, Li H, Lacadie SA, Huang HT, Curran M, Loewer S, Naveiras O, Kathrein KL, Konantz M, Langdon EM, Lengerke C, Zon LI, Collins JJ, Daley GQ.
Cell stem cell. 2012-11-01
PMID: 23122293 | DOI: 10.1016/j.stem.2012.07.018
9. Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells.
Gao P, Chen C, Howell ED, Li Y, Tober J, Uzun Y, He B, Gao L, Zhu Q, Siekmann AF, Speck NA, Tan K.
Genes & development. 2020-06-04
PMID: 32499402 | DOI: 10.1101/gad.338202.120
10. Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells.
Chen C, Yu W, Tober J, Gao P, He B, Lee K, Trieu T, Blobel GA, Speck NA, Tan K.
Cell reports. 2019-12-01
PMID: 31851943 | DOI: 10.1016/j.celrep.2019.11.065
11. De novo generation of macrophage from placenta-derived hemogenic endothelium.
Liang G, Zhou C, Jiang X, Zhang Y, Huang B, Gao S, Kang Z, Ma D, Wang F, Gottgens B, Wang H, Han JJ, Liu F.
Developmental cell. 2021-06-30
PMID: 34197725 | DOI: 10.1016/j.devcel.2021.06.005
12. A single-cell hematopoietic landscape resolves 8 lineage trajectories and defects in Kit mutant mice.
Dahlin JS, Hamey FK, Pijuan-Sala B, Shepherd M, Lau WWY, Nestorowa S, Weinreb C, Wolock S, Hannah R, Diamanti E, Kent DG, Göttgens B, Wilson NK.
Blood. 2018-03-27
PMID: 29588278 | DOI: 10.1182/blood-2017-12-821413
13. Developmental trajectory of prehematopoietic stem cell formation from endothelium.
Zhu Q, Gao P, Tober J, Bennett L, Chen C, Uzun Y, Li Y, Howell ED, Mumau M, Yu W, He B, Speck NA, Tan K.
Blood. 2020-08-01
PMID: 32392346 | DOI: 10.1182/blood.2020004801
14. Tracing the first hematopoietic stem cell generation in human embryo by single-cell RNA sequencing.
Zeng Y, He J, Bai Z, Li Z, Gong Y, Liu C, Ni Y, Du J, Ma C, Bian L, Lan Y, Liu B.
Cell research. 2019-09-09
PMID: 31501518 | DOI: 10.1038/s41422-019-0228-6
15. Decoding human fetal liver haematopoiesis.
Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chédotal A, Roberts I, Göttgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M.
Nature. 2019-10-09
PMID: 31597962 | DOI: 10.1038/s41586-019-1652-y
16. Haematopoietic stem and progenitor cells from human pluripotent stem cells.
Sugimura R, Jha DK, Han A, Soria-Valles C, da Rocha EL, Lu YF, Goettel JA, Serrao E, Rowe RG, Malleshaiah M, Wong I, Sousa P, Zhu TN, Ditadi A, Keller G, Engelman AN, Snapper SB, Doulatov S, Daley GQ.
Nature. 2017-05-17
PMID: 28514439 | DOI: 10.1038/nature22370
17. Conversion of adult endothelium to immunocompetent haematopoietic stem cells.
Lis R, Karrasch CC, Poulos MG, Kunar B, Redmond D, Duran JGB, Badwe CR, Schachterle W, Ginsberg M, Xiang J, Tabrizi AR, Shido K, Rosenwaks Z, Elemento O, Speck NA, Butler JM, Scandura JM, Rafii S.
Nature. 2017-05-17
PMID: 28514438 | DOI: 10.1038/nature22326
18. Regulation of embryonic haematopoietic multipotency by EZH1.
Vo LT, Kinney MA, Liu X, Zhang Y, Barragan J, Sousa PM, Jha DK, Han A, Cesana M, Shao Z, North TE, Orkin SH, Doulatov S, Xu J, Daley GQ.
Nature. 2018-01-17
PMID: 29342143 | DOI: 10.1038/nature25435
19. The N-glycome regulates the endothelial-to-hematopoietic transition.
Kasper DM, Hintzen J, Wu Y, Ghersi JJ, Mandl HK, Salinas KE, Armero W, He Z, Sheng Y, Xie Y, Heindel DW, Park EJ, Sessa WC, Mahal LK, Lebrilla C, Hirschi KK, Nicoli S.
Science (New York, N.Y.). 2020-12-03
PMID: 33273096 | DOI: 10.1126/science.aaz2121
20. CellComm infers cellular crosstalk that drives haematopoietic stem and progenitor cell development.
Lummertz da Rocha E, Kubaczka C, Sugden WW, Najia MA, Jing R, Markel A, LeBlanc ZC, Dos Santos Peixoto R, Falchetti M, Collins JJ, North TE, Daley GQ.
Nature cell biology. 2022-04-12
PMID: 35414020 | DOI: 10.1038/s41556-022-00884-1
21. Mapping human haematopoietic stem cells from haemogenic endothelium to birth.
Calvanese V, Capellera-Garcia S, Ma F, Fares I, Liebscher S, Ng ES, Ekstrand S, Aguadé-Gorgorió J, Vavilina A, Lefaudeux D, Nadel B, Li JY, Wang Y, Lee LK, Ardehali R, Iruela-Arispe ML, Pellegrini M, Stanley EG, Elefanty AG, Schenke-Layland K, Mikkola HKA.
Nature. 2022-04-13
PMID: 35418685 | DOI: 10.1038/s41586-022-04571-x
22. Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization.
Baccin C, Al-Sabah J, Velten L, Helbling PM, Grünschläger F, Hernández-Malmierca P, Nombela-Arrieta C, Steinmetz LM, Trumpp A, Haas S.
Nature cell biology. 2019-12-23
PMID: 31871321 | DOI: 10.1038/s41556-019-0439-6
23. Integrative epigenomic and transcriptomic analysis reveals the requirement of JUNB for hematopoietic fate induction.
Chen X, Wang P, Qiu H, Zhu Y, Zhang X, Zhang Y, Duan F, Ding S, Guo J, Huang Y, Na J.
Nature communications. 2022-06-06
PMID: 35668082 | DOI: 10.1038/s41467-022-30789-4
24. Single-cell transcriptome of early hematopoiesis guides arterial endothelial-enhanced functional T cell generation from human PSCs.
Shen J, Xu Y, Zhang S, Lyu S, Huo Y, Zhu Y, Tang K, Mou J, Li X, Hoyle DL, Wang M, Wang J, Li X, Wang ZZ, Cheng T.
Science advances. 2021-09-03
PMID: 34516916 | DOI: 10.1126/sciadv.abi9787
25. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis.
Ranzoni AM, Tangherloni A, Berest I, Riva SG, Myers B, Strzelecka PM, Xu J, Panada E, Mohorianu I, Zaugg JB, Cvejic A.
Cell stem cell. 2020-12-21
PMID: 33352111 | DOI: 10.1016/j.stem.2020.11.015
26. Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity.
Xia J, Liu M, Zhu C, Liu S, Ai L, Ma D, Zhu P, Wang L, Liu F.
Cell research. 2023-04-04
PMID: 37016019 | DOI: 10.1038/s41422-023-00797-0
27. Establishing a human bone marrow single cell reference atlas to study ageing and diseases.
Lee NYS, Li M, Ang KS, Chen J.
Frontiers in immunology. 2023-03-15
PMID: 37006302 | DOI: 10.3389/fimmu.2023.1127879
28. Single-cell omics identifies inflammatory signaling as a trans-differentiation trigger in mouse embryos.
Zhang Y, Kang Z, Liu M, Wang L, Liu F.
Developmental cell. 2024-03-19
PMID: 38508181 | DOI: 10.1016/j.devcel.2024.02.010
29. Lineage-tracing hematopoietic stem cell origins in vivo to efficiently make human HLF+ HOXA+ hematopoietic progenitors from pluripotent stem cells.
Fowler JL, Zheng SL, Nguyen A, Chen A, Xiong X, Chai T, Chen JY, Karigane D, Banuelos AM, Niizuma K, Kayamori K, Nishimura T, Cromer MK, Gonzalez-Perez D, Mason C, Liu DD, Yilmaz L, Miquerol L, Porteus MH, Luca VC, Majeti R, Nakauchi H, Red-Horse K, Weissman IL, Ang LT, Loh KM.
Developmental cell. 2024-04-02
PMID: 38569552 | DOI: 10.1016/j.devcel.2024.03.003
30. Single-cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity.
Hu C, Zhang N, Hong Y, Tie R, Fan D, Lin A, Chen Y, Xiang LX, Shao JZ.
eLife. 2024-03-18
PMID: 38497789 | DOI: 10.7554/elife.92424
31. Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish.
Rubin SA, Baron CS, Pessoa Rodrigues C, Duran M, Corbin AF, Yang SP, Trapnell C, Zon LI.
The Journal of experimental medicine. 2022-08-08
PMID: 35938989 | DOI: 10.1084/jem.20220038
32. Blood and immune development in human fetal bone marrow and Down syndrome.
Jardine L, Webb S, Goh I, Quiroga Londoño M, Reynolds G, Mather M, Olabi B, Stephenson E, Botting RA, Horsfall D, Engelbert J, Maunder D, Mende N, Murnane C, Dann E, McGrath J, King H, Kucinski I, Queen R, Carey CD, Shrubsole C, Poyner E, Acres M, Jones C, Ness T, Coulthard R, Elliott N, O'Byrne S, Haltalli MLR, Lawrence JE, Lisgo S, Balogh P, Meyer KB, Prigmore E, Ambridge K, Jain MS, Efremova M, Pickard K, Creasey T, Bacardit J, Henderson D, Coxhead J, Filby A, Hussain R, Dixon D, McDonald D, Popescu DM, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Regev A, Behjati S, Laurenti E, Wilson NK, Roy A, Göttgens B, Roberts I, Teichmann SA, Haniffa M.
Nature. 2021-09-29
PMID: 34588693 | DOI: 10.1038/s41586-021-03929-x
33. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris.
Tabula Muris Consortium, Overall coordination, Logistical coordination, Organ collection and processing, Library preparation and sequencing, Computational data analysis, Cell type annotation, Writing group, Supplemental text writing group, Principal investigators.
Nature. 2018-10-03
PMID: 30283141 | DOI: 10.1038/s41586-018-0590-4
34. Mapping the Mouse Cell Atlas by Microwell-Seq.
Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, Huang D, Xu Y, Huang W, Jiang M, Jiang X, Mao J, Chen Y, Lu C, Xie J, Fang Q, Wang Y, Yue R, Li T, Huang H, Orkin SH, Yuan GC, Chen M, Guo G.
Cell. 2018-02-01
PMID: 29474909 | DOI: 10.1016/j.cell.2018.02.001
35. A Mettl16/m6A/mybl2b/Igf2bp1 axis ensures cell cycle progression of embryonic hematopoietic stem and progenitor cells.
Han Y, Sun K, Yu S, Qin Y, Zhang Z, Luo J, Hu H, Dai L, Cui M, Jiang C, Liu F, Huang Y, Gao P, Chen X, Xin T, Ren X, Wu X, Song J, Wang Q, Tang Z, Chen J, Zhang H, Zhang X, Liu M, Luo D.
The EMBO journal. 2024-04-11
PMID: 38605226 | DOI: 10.1038/s44318-024-00082-9
36. The RNA-binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling.
Li Y, Li C, Liu M, Liu S, Liu F, Wang L.
Development (Cambridge, England). 2023-10-24
PMID: 37874038 | DOI: 10.1242/dev.201890
37. Multilayer omics analysis reveals a non-classical retinoic acid signaling axis that regulates hematopoietic stem cell identity.
Schönberger K, Obier N, Romero-Mulero MC, Cauchy P, Mess J, Pavlovich PV, Zhang YW, Mitterer M, Rettkowski J, Lalioti ME, Jäcklein K, Curtis JD, Féret B, Sommerkamp P, Morganti C, Ito K, Ghyselinck NB, Trompouki E, Buescher JM, Pearce EL, Cabezas-Wallscheid N.
Cell stem cell. 2021-10-26
PMID: 34706256 | DOI: 10.1016/j.stem.2021.10.002
38. The ATF4-RPS19BP1 axis modulates ribosome biogenesis to promote erythropoiesis.
Zheng Z, Yang S, Gou F, Tang C, Zhang Z, Gu Q, Sun G, Jiang P, Wang N, Zhao X, Kang J, Wang Y, He Y, Yang M, Lu T, Lu S, Qian P, Zhu P, Cheng H, Cheng T.
Blood. 2024-04-24
PMID: 38657191 | DOI: 10.1182/blood.2023021901
39. Single-cell transcriptomic landscape of human blood cells.
Xie X, Liu M, Zhang Y, Wang B, Zhu C, Wang C, Li Q, Huo Y, Guo J, Xu C, Hu L, Pang A, Ma S, Wang L, Cao W, Chen S, Li Q, Zhang S, Zhao X, Zhou W, Luo H, Zheng G, Jiang E, Feng S, Chen L, Shi L, Cheng H, Hao S, Zhu P, Cheng T.
National science review. 2020-08-24
PMID: 34691592 | DOI: 10.1093/nsr/nwaa180
40. Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging.
Bandyopadhyay S, Duffy MP, Ahn KJ, Sussman JH, Pang M, Smith D, Duncan G, Zhang I, Huang J, Lin Y, Xiong B, Imtiaz T, Chen CH, Thadi A, Chen C, Xu J, Reichart M, Martinez Z, Diorio C, Chen C, Pillai V, Snaith O, Oldridge D, Bhattacharyya S, Maillard I, Carroll M, Nelson C, Qin L, Tan K.
Cell. 2024-05-06
PMID: 38714197 | DOI: 10.1016/j.cell.2024.04.013
41. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia.
Granja JM, Klemm S, McGinnis LM, Kathiria AS, Mezger A, Corces MR, Parks B, Gars E, Liedtke M, Zheng GXY, Chang HY, Majeti R, Greenleaf WJ.
Nature biotechnology. 2019-12-02
PMID: 31792411 | DOI: 10.1038/s41587-019-0332-7
42. Identification of phenotypically, functionally, and anatomically distinct stromal niche populations in human bone marrow based on single-cell RNA sequencing.
Li H, Bräunig S, Dhapolar P, Karlsson G, Lang S, Scheding S.
eLife. 2023-03-06
PMID: 36876630 | DOI: 10.7554/elife.81656
43. Decoding human fetal liver haematopoiesis.
Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chédotal A, Roberts I, Göttgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M.
Nature. 2019-10-09
PMID: 31597962 | DOI: 10.1038/s41586-019-1652-y