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Series GSE87104 Query DataSets for GSE87104
Status Public on May 10, 2017
Title RNA-seq Analysis of Wild Type and Ptpn11-deficient cerebellar Transcriptomes
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We have recently discovered that deletion of Ptpn11, which codes for protein tyrosine phosphatase Shp2, blocks Bergmann glia (BG) formation and cerebellar foliation, whereas expressing a constitutively active Mek1 (Map2k1), Mek1DD, reverses the Ptpn11-deficient phenotypes, uncovering a previously unappreciated role of BG in folding of the cerebellar cortex. Relatively little is known regarding to the BG induction. The goal of the study was to determine molecular features of newly generated BG.
To identify transcripts enriched in nascent BG, we performed RNA-seq of microdissected cerebellar tissues from wild type (WT), En1cre/+;Ptpn11F/F (Ptpn11-cKO), and En1cre/+;Ptpn11F/F;R26Mek1DD/+ (Ptpn11-cKO;MEK) embryos at E12.5, E13.5, and E14.5.
As BG are initially formed at E13.5, we reasoned that BG-enriched transcripts should be increased from E12.5 to E14.5, decreased in Ptpn11-cKO cerebella, and restored in Ptpn11-cKO;MEK cerebella. By intersecting differentially expressed (DE) genes based on the above-mentioned assumptions, we wanted to identify genes that are specifically expressed in BG and affected by Ptpn11 deletion.
Conclusions: though RNA-seq and subsequent validation, we have successfully identified genes that enriched in nascent BG in the developing mouse cerebellum.
Overall design The transcriptome of the cerebellum of mid-gestation stage mouse embryos were generated by deep sequencing.
Contributor(s) Li J
Citation(s) 28489004
Submission date Sep 19, 2016
Last update date May 15, 2019
Contact name James YH Li
Organization name UCHC
Department Genetics and Genome Sciences
Street address 263 Farmington Ave
City Farmington
State/province CT
ZIP/Postal code 06117
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (28)
GSM2322423 CKO.1
GSM2322424 CKO.2
GSM2322425 CKO.3
BioProject PRJNA343552
SRA SRP090141

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Supplementary file Size Download File type/resource
GSE87104_rawCounts.csv.gz 1.2 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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