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Series GSE109196 Query DataSets for GSE109196
Status Public on Nov 14, 2018
Title Comparing the Transcriptomes of Marf1 wildtype (WT) oocytes with those of Marf1-genetrap (GT-Mut) and Marf1-D272 mutant(D272-Mut) oocytes by RNA-Seq Analysis
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The goal of this study is to reveal the globle changes of oocyte transcriptome after mutations of Marf1 either by gene trap or knockin of point mutation by comparing the corresponding transcriptomes via RNA-Seq Analysis.
Overall design Marf1 wildtype (WT), Marf1-genetrap (GT-Mut), and Marf1-D272 mutant(D272-Mut) GV-stageFGOs were collected in RLT lysis buffer for RNA-Seq analysis. 4 replictates of each treatment, with 80 oocyte per samples, were collected for the experiment. Total RNA was extracted with RNeasy Micro Kit (Qiagen, Germantown, MD, USA) according to manufacturer's instructions, and 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 oocyte 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) 30333187
Submission date Jan 15, 2018
Last update date Mar 01, 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)
GSM2935126 GTMut1
GSM2935127 GTMut2
GSM2935128 GTMut3
This SubSeries is part of SuperSeries:
GSE109213 Assessing the effect of D272A-mutation of MARF1 on oocyte transcriptome
BioProject PRJNA430085
SRA SRP130984

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Supplementary file Size Download File type/resource
GSE109196_WT-Mut_FPKM_DEG_Summary.xlsx 4.4 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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