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JOHN DICK’S  LABORATORY

Research Data Portal

Companion website for paper by Laurenti et al.  

Our laboratory generated gene expression profiles for 10 highly purified human hematopoieitic stem and progenitor cells from cord blood. Gene expression profiling was performed on Illumina arrays with a protocol optimized for maximal sensitivity on low number of cells.

This data set provides a comprehensive description of the cellular and molecular architecture of the initial steps of stem cell differentiation and lineage commitment in human hematopoiesis. Here we present a portal with pre-processed data files, which should facilitate further interrogation of the dataset. 

 

 

 

 

 

 

 

 

 

 

Click on the links below to download normalized and processed data pertaining to this dataset. Raw data is available on the GEO website (accession number: GSE42414 ) 

All differentially expression lists below were generated with the limma algorithm in R/Bioconductor as described in this table: ContrastsUsedInLaurentiEtAl.docx

 

- Normalized log2-transformed signal for all samples analyzed in the study:

             NormLog2Expression_AllSamples.xlsx

- Normalized log2-transformed signal averaged for each population in the study:

ExprMx.xlsx

 

- Population-specific contrasts

HSC: 10pops_38_HSC.xlsx

MLP: 10pops_39_MLP.xlsx

CMP: 10pops_40_CMP.xlsx

GMP: 10pops_41_GMP.xlsx

MEP: 10pops_42_MEP.xlsx

B-NK progenitor: 10pops_43_BNKprog.xlsx

ProB: 10pops_44_ProB.xlsx

ETP: 10pops_45_ETP.xlsx

From these, the top 250 genes significantly upregulated in each population, constitute population-specific signatures tat can be used for Gene Set Enrichment Analysis (GSEA).

PopSpecificSignatures_250.xls

 

- Transcriptional programs contrasts: represent transcriptional programs shared by several populations across the human hematopoietic hierarchy.

HSC-MLP transcriptional program: Sign06_HSC_MLP.xlsx

MLP-GMP transcriptional program: Sign11_MLP_GMP.xlsx

HSC-MLP-GMP transcriptional program: Sign17_HSC_MLP_GMP.xlsx

 

- Precursor-product transition gene-sets: represent genes that are changed between 2 developmentally related populations.

HSC1 to HSC2: HSC1toHSC2_26.xlsx

HSC1 to MPP: HSC1toMPP_27.xlsx

HSC1 to MLP: HSC1toMLP_28.xlsx

HSC1 to CMP: HSC1toCMP_29.xlsx

MPP to MLP: MPPtoMLP_30.xlsx

MPP to CMP: MPPtoCMP_31.xlsx

MLP to B-NK progenitor: MLPtoBNKprec_32.xlsx

MLP to ProB: MLPtoProB_33.xlsx

MLP to ETP: MLPtoETP_34.xlsx

MLP to GMP: MLPtoGMP_46.xlsx

B-NK progenitor to ProB: BNKprectoProB_35.xlsx

CMP to GMP: CMPtoGMP_36.xlsx

CMP to MEP: CMPtoMEP_37.xlsx