Transcriptomics

Dataset Information

24

Isolation and transcriptional profiling of embryonic human neural crest cells


ABSTRACT: To identify new candidate genes for neurocristopathies, a Long-SAGE library has been made from human neural crest cells (hNCC) derived from a normal embryo at Carnegie stage 13. Data analysis indicates the expression of a number of genes in multiple GO functional classes that were anticipated based on animal studies and/or human disease. An average linkage hierarchical clustering was performed using SAGE data from hNCC and 14 other normal tissues and cell lines. This and other analyses indicate a high degree of molecular identity between hNCC and the two human embryonic stem cells (hES) lines included, compared to the other tissue or cell types included, including more tissue-restricted stem cells, such as mesenchymal stem cells, or hNCC derivatives such as Schwann cells. Keywords: Cell type comparison Overall design: Total RNA was extracted from a confluent 10 cm dish of hNCC (line N5) from a female human embryo at 28-32 dpf (Carnegie stage 13). Half the RNA was used to construct a SAGE bank with long tags using NlaIII and MmeI. Data was then compared to currently publicly available SAGE data from fourteen banks made from normal human tissues for hierarchical clustering. Third-party GEO accession numbers for human SAGE data: GSM41360, hES3; GSM41362, hES4; GSM48250, sciatic nerve; GSM48251, Schwann cells (in vitro); GSM31931, brain substantia nigra; GSM824, muscle; GSM785, liver; GSM708, kidney; GSM676, brain white matter; GSM761, brain cerebellum; GSM762, lung. Other third-party data: Cancer Genome Anatomy Project http://cgap.nci.nih.gov/SAGE/SAGELibraryFinder: SAGE_Prostate_normal_B_2 (prostate) Umbilical cord- and bone marrow-derived mesenchymal stem cell data had been downloaded from currently broken links http://bit.fmrp.usp.br/uc-msc_tags/ and http://bit.fmrp.usp.br/msc_tags/ as referenced in Panepucci et al. (2004) Stem Cells 22:1263-1278; DOI: 10.1634/stemcells.2004-0024 (UC-MSC) and Silva et al. (2003) Stem Cells 21:661-669.

INSTRUMENT(S): SAGE:17:NlaIII:Homo sapiens

ORGANISM(S): Homo sapiens  

SUBMITTER: Heather C Etchevers  

PROVIDER: GSE8368 | GEO |

SECONDARY ACCESSION(S): PRJNA101395

REPOSITORIES: GEO

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