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Series GSE67120 Query DataSets for GSE67120
Status Public on May 19, 2016
Title Tracing the Formation of Haematopoietic Stem Cells in Mouse Embryos by Single-cell Functional and RNA-Seq Analyses [single-cell]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Haematopoietic stem cells (HSCs) are derived early from embryonic precursor cells, such as haemogenic endothelial cells and pre-HSCs. However, the identity of precursor cells remains elusive due to their rareness, transience, and inability to be isolated efficiently. Here we employed potent surface markers to capture the nascent pre-HSCs at 30% purity, as rigorously validated by single-cell-initiated serial transplantation assay. Then we applied single-cell RNA-Seq technique to analyse five populations closely related to HSC formation: endothelial cells, CD45- and CD45+ pre-HSCs in E11 aorta-gonad-mesonephros (AGM) region, and mature HSCs in E12 and E14 foetal liver. In comparison, the pre-HSCs showed unique features in transcriptional machinery, apoptosis, metabolism state, signalling pathway, transcription factor network, and lncRNA expression pattern. Among signalling pathways enriched in pre-HSCs, the mTOR activation was uncovered indispensable for the emergence of HSCs but not haematopoietic progenitors from endothelial cells in vivo. By comparing with proximal populations without HSC potential, the core molecular signature of pre-HSCs was identified. Collectively, our work paves the way for dissection of complex molecular mechanisms regulating the step-wise generation of HSCs in vivo, informing future efforts to engineer HSCs for clinical application.
Overall design RNA-Seq of 181 single-cell samples from 8 FACS sorted cell types:
1. endothelial cells (samples E11.0_EC_xxxx. CD31+ VE-cadherin+CD41-CD43-CD45-Ter119-);
2. T1 pre-HSCs (samples E11.0_T1_xxxx. CD31+CD45-CD41low c-Kit+CD201high);
3. T1 CD201- cells (samples E11.0_T1CD201neg_xxxx, CD31+CD45-CD41low c-Kit+CD201low/-) ;
4. T2 pre-HSCs (samples E11.0_T2_35xx. CD31+CD45+c-Kit+CD201high),
5. T2 CD41low (samples E11.0_T2_21xx, E11.0_T2_24xx and E11.0_T2_27xx. CD31+CD45+CD41low);
6. E12 HSCs (samples E12.5_FL_xxxx. Lin-Sca-1+Mac-1lowCD201+);
7. E14 HSCs (samples E14.5_FL_xxxx. CD45+CD150+CD48-CD201+);
8. Adult HSCs (samples Adult_HSC_xxxx. CD45+CD150+CD48-CD201+).

ECs, T1 pre-HSCs, T1 CD201- cells, T2 pre-HSCs, T2 CD41low cells were sorted from E11 AGM region. Mature HSCs were sorted from E12 or E14 fetal liver and adult bonemarrow.
Contributor(s) Zhou F, Li X, Zhu P, Zhou J, Ding M, Xiong F, Zheng X, Li Z, Ni Y, Wen L, Liu B, Tang F
Citation(s) 27225119
Submission date Mar 20, 2015
Last update date May 15, 2019
Contact name Xianlong Li
Organization name Peking University
Department Biodynamic Optical Imaging Center, College of Life Sciences
Street address 5, Yiheyuan Rd., Haidian District
City Beijing
ZIP/Postal code 100871
Country China
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (181)
GSM1639559 E11.0_EC_3205
GSM1639560 E11.0_EC_3207
GSM1639561 E11.0_EC_3208
This SubSeries is part of SuperSeries:
GSE67123 Tracing the formation of hematopoietic stem cells in mouse embryos by single-cell functional and RNA-Seq analyses
BioProject PRJNA279003
SRA SRP056386

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE67120_ERCC_Controls_Annotation_ERCC_RNA_Spike-In_Control_Mixes.txt.gz 25.3 Kb (ftp)(http) TXT
GSE67120_RAW.tar 102.4 Mb (http)(custom) TAR (of FPKM_TRACKING)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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