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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.
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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
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|
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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 |