GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE109195 Query DataSets for GSE109195
Status Public on Nov 14, 2018
Title Comparing the Transcriptomes of Marf1-genetrap (GT) oocytes with those microinjected with mRNAs for wild type MARF1 (GTWT) or D272-mutated MARF1 (GTD272) 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 effect of supplementation with either wild type MARF1or D272-mutated MARF1 on the steady-state levels of mRNAs in Marf1-gene trap GV-stage fully-grown oocytes(FGOs) by comparing the corresponding transcriptomes via RNA-Seq Analysis.
Overall design Marf1-genetrap (GT) GV-stageFGOs were microinjected with mRNAsencoding wild type MARF1 or D272-mutated MARF1, and cultured for 48 h in milrinone supplemented medium. Then the oocytes 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)
GSM2935114 GT1
GSM2935115 GT2
GSM2935116 GT3
This SubSeries is part of SuperSeries:
GSE109213 Assessing the effect of D272A-mutation of MARF1 on oocyte transcriptome
BioProject PRJNA430084
SRA SRP130983

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
GSE109195_GT-mRNA_FPKM_DEG_Summary.xlsx 4.6 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap