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Series GSE55981 Query DataSets for GSE55981
Status Public on Apr 07, 2016
Title Cell cycle-independent temporal identity transitions in cortical progenitor cells as revealed by single cell transcriptome analysis
Organism Mus musculus
Experiment type Expression profiling by array
Summary During cerebral development, a variety of neurons are sequentially generated by self-renewing progenitor cells, apical progenitors (APs). A temporal change in AP identity is thought to produce a diversity of progeny neurons, while underlying mechanisms are largely unknown. Here we performed single cell genome-wide transcriptome profiling of APs at different neurogenic stages, and identified a set of genes that are temporally expressed in APs in a manner independent of differentiation state. Surprisingly, the temporal pattern of such AP gene expression was not affected by arresting cell cycling. Consistently, a transient cell cycle arrest of APs in vivo did not prevent descendant neurons to acquire their correct laminar fates. in vitro cell culture of APs revealed that transitions in AP gene expression involved in both cell-autonomous and non-autonomous mechanisms. These results suggest that timers controlling AP temporal identity run independently of cell cycle progression and Notch activation mode. 
 
Overall design We randomly picked up single cells from dorso-lateral portion of cerebral wall of a CD1 mouse at E11, E12 or small VZ/SVZ fragments of the same portion at E14 (3 days after in vivo electroporation of pCAG-NICD and pEF-p18) and E16. In 3 cases, cells are picked up from 3-days-in-vitro neurospheres derived from E11 dorso-lateral portion of cerebral wall. Single-cell cDNA samples were generated and amplified as descibed (Kurimoto et al.Nucreic Acid Res.34:e42, 2006). After checking the quality of the samples, we then chose 30 (E11), 3 (APs from E12), 28 (E16), 4 (E14, NICD+p18 overexpressed APs), and 3 (APs from 3 days-in-vitro neurosphere) samples and applied them to GeneChip analysis. We then performed analysis with these samples in addition to previously obtained data with E14 samples, which were deposited to GEO as GSE10881.
 
Contributor(s) Okamoto M, Miyata T, Konno D, Ueda HR, Kasukawa T, Matsuzaki F, Kawaguchi A
Citation(s) 27094546
Submission date Mar 18, 2014
Last update date Feb 11, 2019
Contact name Takeya Kasukawa
Organization name RIKEN
Department Center for Integrative Medical Sciences
Lab Large Scale Data Managing Unit
Street address 1-7-22, Suehiro-cho, Tsurumi-ku
City Yokohama, Kanagawa
ZIP/Postal code 2300045
Country Japan
 
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (68)
GSM1349762 cell_E11-30F
GSM1349763 cell_E11-30L
GSM1349764 cell_E11-31i
Relations
BioProject PRJNA241510

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE55981_RAW.tar 253.9 Mb (http)(custom) TAR (of CEL, CHP)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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