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RNA‐seq to identify novel markers for neural tissue differentiation (LB211)
Author(s) -
Giorda Kristina,
Sun Yongming,
Frey Elizabeth,
Taylor Madison,
Barron Tori,
Piper David,
Meredith Gavin
Publication year - 2014
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.28.1_supplement.lb211
Subject(s) - biology , transcriptome , induced pluripotent stem cell , neural stem cell , homeobox protein nanog , cellular differentiation , population , rna , stem cell marker , embryonic stem cell , stem cell , microbiology and biotechnology , computational biology , genetics , gene expression , gene , demography , sociology
Neural tissue differentiated and cultured from patient‐derived stem cells is expected to revolutionize the treatment of patients with brain and spinal injuries and diseases. Critical for these cellular therapies is accurate control and monitoring of differentiation but current methods for such cell typing are limited to qPCR and immunocytochemisty (ICC) which is not sufficient to discriminate between the numerous (likely >100,000) possible neural cell‐types. RNA(transcriptome aka RNA‐Seq) profiling permits the characterization and discovery of much‐needed novel markers. To define the temporal transcriptional signature of neural stem cells, cultured human embryonic stem cells (H9) were compared to induced neural stem cells (NSCs) at d0, d7 and d14. ICC was performed on the putative NSC pools at d7 and d14 for markers of pluripotency (Oct4) and neural differentiation (nestin, Sox1, and Pax6) and H9 cells were stained on d14 for markers of pluripotency (Oct4 and SSEA4). Total RNA was isolated over the time course from the undifferentiated and differentiated cells. Ion Torrent libraries were created to profile expression of miRNAs and whole transcriptomes for each cell population. Multiplexed Proton sequencing and Torrent Suite Software analysis yielded 蠅2.5 million small RNA reads and 蠅29 million whole transcriptome reads per sample. Cluster analysis of the RNA‐Seq profiles indicates that the cell populations have characteristic molecular signatures. Among genes that are decreased in induced cells are OCT4 (POU5F1), JARID2, NANOG , consistent with the differentiation of iPSCs into neurons. Among genes that showed increased expressions are NTRK2, POU3F2, and a number of HOX family genes. We also find lincRNA are involved in cell differentiation.