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Sample GSM4189574 Query DataSets for GSM4189574
Status Public on Apr 02, 2022
Title zygote-siCtrl-2
Sample type SRA
 
Source name Mouse embryo
Organism Mus musculus
Characteristics tissue: Mouse embryo
development stage: Late zygote stage (14 hr post fertilization)
overexpression: siCtrl
strain: B6D2F1 (C57BL/6xDBA/2)
Treatment protocol Embryos were treated with 0.5% protease E to remove zona pellucida and the released blastomeres were washed thoroughly in PBS with 0.5% BSA.
Growth protocol After siRNA injection, GV-stage oocytes were incubated in αMEM medium with 5% FBS and 1.5 IU/ml hCG for in vitro maturation. Then the matured MII oocytes were incubated with sperm for in vitro fertilization. The fertilized embryos were cultured in Q2 medium until harvested.
Extracted molecule genomic DNA
Extraction protocol Harvested blastomeres were placed into lysis buffer, and Superscript II-triggered reverse transcription followed by cDNA amplification were performed. The amplified cDNA was then fragmented using a Covaris sonicator.
The fragmented DNA were subjected to library construction using KAPA Hyper Prep Kit for the Illumina platform, following the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source genomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using STAR (v2.5.2b) with default parameters.
Gene expression for each sample was quantified to TPM using stringtie v1.3.4.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each transcript.
 
Submission date Nov 22, 2019
Last update date Apr 04, 2022
Contact name Shaorong Gao
Organization name Tongji University
Department School of life science and technology
Lab Gaolab
Street address 1239 Siping Road, Yangpu District
City Shanghai
State/province Shanghai
ZIP/Postal code 200092
Country China
 
Platform ID GPL13112
Series (2)
GSE140876 Nucleosome organization dynamics during fertilization reveals regulation factors of zygotic gene activation in mouse (RNA-seq)
GSE140877 Nucleosome organization dynamics during fertilization reveals regulation factors of zygotic gene activation in mouse
Relations
BioSample SAMN13353777
SRA SRX7202739

Supplementary file Size Download File type/resource
GSM4189574_zygote-siCtrl-2.gene.gtf.gz 3.9 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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