Internal Dataset
Developmental differences between neonatal and adult human erythropoiesis.
UID: 10376
- Description
- RNA was extracted from FACS-sorted cells at 8 distinct stages of erythropoiesis, derived from CB- and PB-CD34+ cells. cDNA libraries were prepared using the Illumina TruSeq kit and sequenced on the Illumina HiSeq 2500 (Epigenomics Core of Weill Cornell Medical College, New York). This sequencing strategy produced ~15-80 million 50bp single end reads per sample. For each distinct stage of erythropoiesis, 3 biological replicates were obtained from independently cultured and sorted samples from different donations. Quality control of reads was performed and low-quality reads removed. Reads were aligned to the hg19 reference genome using HISAT2. Raw read counts were extracted from the aligned reads using the featureCounts program. Differential expression analysis was done at each stage comparing the two original sources of CD34+ cells using the DESeq2 bioconductor package. Using gene expression data from each stage, the subset of genes differentially expressed as a function of HSPC source was clustered using divisive hierarchical clustering and split into 10 clusters. Gene ontology enrichment analysis of the biological process gene sets was then performed on each cluster using the cluster Profiler R package with the gene background of all genes expressed across all stages in both sources.
- Local Expert
Newborn (under 1 month)
Access
- Restrictions
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Free to All
- Instructions
- GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.
- Grant Support
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P01 DK032094/National Institute of Diabetes and Digestive and Kidney Diseases
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