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Series GSE98497 Query DataSets for GSE98497
Status Public on Jun 01, 2018
Title Comparing the Transcriptomes of Wild Type and Mtor-Gdf9-Cre mediated Oocyte-Conditional Knockout Mouse ovaries 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 mediated Mtor oocyte-specific knockout (CKO) ovaries by comparing the transcriptomes of Mtor Wild-Type (WT) and CKO Mouse ovaries via RNA-Seq Analysis.
Overall design Seven WT- and 5 Mtor-CKO ovarian samples were collected from 6-month old mice that were initially primed with eCG (5 IU/mouse) for 46 h. Total RNA was extracted with RNeasy Mini Kit (Qiagen, Germantown, MD, USA) according to manufacturer's instructions, and 500 ng was then taken out from each of them and subjected to mRNA isolation using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, Ipswich, MA, USA). The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment. The ovarian mRNA libraries were sequenced on an Illumina 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 03, 2017
Last update date May 15, 2019
Contact name You-Qiang Su
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 (12)
GSM2597420 CKO_1
GSM2597421 CKO_2
GSM2597422 CKO_3
BioProject PRJNA385270
SRA SRP106322

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Supplementary file Size Download File type/resource
GSE98497_FPKM_DEG_Summary.txt.gz 1.2 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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