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Series GSE72857 Query DataSets for GSE72857
Status Public on Nov 25, 2015
Title Transcriptional heterogeneity and lineage commitment in myeloid progenitors [single cell RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Within the bone marrow, hematopoietic stem cells differentiate and give rise to diverse blood cell types and functions. Currently, hematopoietic progenitors are defined using surface markers combined with functional assays that are not directly linked with the in vivo potential or gene regulatory mechanisms. Here we comprehensively identify myeloid progenitor subpopulations by transcriptional sorting of single cells from the bone marrow. We describe multiple progenitor subgroups showing unexpected transcriptional priming towards seven differentiation fates, but no progenitors with a mixed state. Transcriptional differentiation is correlated with combinations of known and previously undefined transcription factors, suggesting the process is tightly regulated. Histone maps and knockout assays are consistent with the transcriptional states while traditional transplantation experiments are only partially overlapping myeloid transcriptional priming. Our analyses uncover the function of the underlying regulatory mechanisms for several sub groups and establishes a general framework for dissecting hematopoiesis.
 
Overall design Bone marrow Lin- cKit+ Sca1- myeloid progenitors mRNA profiles from single cells were generated by deep sequencing of thousands of single cells, sequenced in several batches in an Illumina NextSeq

Please note that [1] raw data files were processed as single-ended file since second read (mate) files contain only cell/molecule barcodes and therefore, not provided. This information was appended to the fastq entry header [2] The 'experimental_design.txt' file explains the correspondence of each single cell (WXXXX) in the 'umitab.txt' to a sample (ABXXXX).
 
Contributor(s) Amit I, Tanay A, Paul F, Arkin Y, Giladi A
Citation(s) 26627738
Submission date Sep 09, 2015
Last update date Mar 22, 2019
Contact name Ido Amit
E-mail ido.amit@weizmann.ac.il
Phone 972-8-9343338
Organization name Weizmann Institute of Science
Department Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 760001
Country Israel
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (54)
GSM1873450 AB167 [Sample 1]
GSM1873451 AB168 [Sample 2]
GSM1873452 AB173 [Sample 3]
This SubSeries is part of SuperSeries:
GSE72859 Transcriptional heterogeneity and lineage commitment in myeloid progenitors
Relations
BioProject PRJNA295200
SRA SRP063520

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
GSE72857_experimental_design.txt.gz 113.2 Kb (ftp)(http) TXT
GSE72857_umitab.txt.gz 15.7 Mb (ftp)(http) TXT
Raw data are available in SRA
Processed data is available on Series record

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