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Sample GSM8169599 Query DataSets for GSM8169599
Status Public on Sep 09, 2024
Title Day-14-Total-RNA-MTR4-null-Cytoplasm-rep1
Sample type SRA
 
Source name Oocyte
Organism Mus musculus
Characteristics tissue: Oocyte
cell compartment: Cytoplasm
genotype: Mtr4-null
Extracted molecule total RNA
Extraction protocol Oocytes were collected from indicated genotypes from mice of different stages. Then nucleus-cytoplasm separation were performed with micromanipulation. Nuclei and cytoplasm were collected separately.
After sample collection,total RNA were extracted using TRIzol. Purified total RNA were firstly removed rRNAs using the Abclonal rRNA Depletion module, total RNA was used as input for library construction using the Abclonal Fast RNA-seq Lib Prep Kit V2. DNA fragments were selected,and the final sequencing libraries were constructed from 300–400 bp of the amplified cDNAs. Sequencing data were extracted on the Illumina HiSeq X Ten platform in the 150 bp paired-end mode.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing RNA-Seq was performed with biological replicates for all samples.
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1.
Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Expression level was further normalized with the ERCC spike-in.
Assembly: mm9
Supplementary files format and content: txt file includes processed FPKM with ERCC correlation for each sample
 
Submission date Mar 25, 2024
Last update date Sep 09, 2024
Contact name Heng-yu Fan
E-mail(s) Fanhengyu_lab@163.com, 21907079@zju.edu.cn
Organization name Life Sciences Institute
Lab Fan heng-yu
Street address Yuhangtang Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310058
Country China
 
Platform ID GPL21273
Series (2)
GSE247852 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes
GSE262431 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [day 14 total_RNA-seq-Nu_Cy]
Relations
BioSample SAMN40608626
SRA SRX24051165

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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