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Series GSE114126 Query DataSets for GSE114126
Status Public on Jun 01, 2018
Title Comparing the Transcriptomes of Wild Type (WT) and Gdf9-Cre or Zp3-Cre mediated Mtor Oocyte-Conditional Knockout (referred to as MG and MZ, respectively) Mouse GV-stage fully-grown oocytes (FGO) by RNA-Seq Analysis
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The goal of this study is to identify the differentially expressed genes in Gdf9-Cre and Zp3-Cre mediated Mtor oocyte-specific knockout (CKO) GV-stage fully-grown oocytes (FGO) by comparing their transcriptomes with that of the wild-type (WT) via RNA-Seq Analysis.
 
Overall design Methods: mRNA profiles of 3 sets of GV-stage FGOs collected from the large antral follicles of 23-day old WT-, MG-, and MZ- CKO female mice were generated by deep sequencing using HiSeq X Ten platform with 150bp pair-end reads. All reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads were then aligned to the mm10 reference genome using tophat2 (v2.0.13), and FPKMs were calculated and normalized using cufflinks (v2.2.1). The differentially expressed genes were calculated using default parameter of cuffdiff (v2.2.1). Hierarchical clustering was carried on log2(FPKM+1) across samples. Genes used for clustering were selected by maximum FPKM≥1 and with top 10% standard deviation of log2(FPKM+1).
 
Contributor(s) Su Y
Citation(s) 29784807
Submission date May 07, 2018
Last update date Mar 01, 2019
Contact name You-Qiang Su
E-mail(s) youqiang.su@njmu.edu.cn
Organization name Nanjing Medical University
Department State Key Laboratory of Reproductive Medicine
Street address 140 Hanzhong Road
City Nanjing
State/province Jiangsu
ZIP/Postal code 210029
Country China
 
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (9)
GSM3133292 WT-1
GSM3133293 WT-2
GSM3133294 WT-3
Relations
BioProject PRJNA464376
SRA SRP144775

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

Supplementary file Size Download File type/resource
GSE114126_FPKM_DEG_Summary.txt.gz 1.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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