Transcriptomics

Dataset Information

102

RNA-seq analysis of differentiating human erythroblasts


ABSTRACT: Human erythroblasts purified from cord blood were cultured in vitro and FACS-sorted into five highly purified populations representing distinct differentiation stages:  proerythroblasts, early basophilic erythroblasts, late basophilic erythroblasts, polychromatophilic erythroblasts, and orthochromatophilic erythroblasts. The methods for culture and sorting experiments are given in Hu et al. 2013. For each RNA-seq library, RNA was isolated from 1x 106 sorted human erythroblasts using RNeasy Plus Mini kits (Qiagen). Libraries were then prepared using Illumina TruSeqTM RNA kits to obtain 50 nt reads. Collaborators at the New Your Blood Center were responsible for erythroblast culture, FACS purification of erythroblast populations, and acquisition of RNA-seq data. Collaborators at U.C. Berkeley and Lawrence Berkeley National Laboratory performed data analysis and experimental validation of alternative splicing in erythroblasts. Results: Differentiating erythroblasts execute a dynamic alternative splicing program that is enriched in genes affecting cell cycle, organelle organization, chromatin function, and RNA processing. Alternative splicing plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells. Erythroid differentiation stage-specific transcriptome analysis was performed by RNA-seq analysis of highly purified erythroblast populations

ORGANISM(S): Homo sapiens  

SUBMITTER: John G Conboy  Xiuli An   Lior Pachter   Dana Ghanem   Harold Pimentel   Jie Li   Sherry Gee   Marilyn Parra   Narla Mohandas    

PROVIDER: E-GEOD-53635 | ArrayExpress| 2014-04-15

SECONDARY ACCESSION(S): SRP034711GSE53635PRJNA232527

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis.

Pimentel Harold H   Parra Marilyn M   Gee Sherry S   Ghanem Dana D   An Xiuli X   Li Jie J   Mohandas Narla N   Pachter Lior L   Conboy John G JG  

Nucleic acids research 20140117 6


Alternative pre-messenger RNA splicing remodels the human transcriptome in a spatiotemporal manner during normal development and differentiation. Here we explored the landscape of transcript diversity in the erythroid lineage by RNA-seq analysis of five highly purified populations of morphologically distinct human erythroblasts, representing the last four cell divisions before enucleation. In this unique differentiation system, we found evidence of an extensive and dynamic alternative splicing p  ...[more]

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