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Sample GSM5728984 Query DataSets for GSM5728984
Status Public on Oct 10, 2022
Title RTCB-KO-6W-1
Sample type SRA
 
Source name Fully-grown GV oocyte
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: oocyte
developmental stage: Fully-grown GV
genotype/variation: Rtcb knock-out
Extracted molecule polyA RNA
Extraction protocol Oocytes were collected from indicated genotypes (10 oocytes per sample) after PMSG treatment for 44-48h. Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description RTCB.FPKM.normbyERCC.txt
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.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples
 
Submission date Dec 10, 2021
Last update date Oct 10, 2022
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 (1)
GSE190681 RNA Ligase RTCB-mediated mRNA Alternative Splicing is Required for Mouse Oocyte Development and Maintenance
Relations
BioSample SAMN23893680
SRA SRX13379874

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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