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Sample GSM5531283 Query DataSets for GSM5531283
Status Public on May 21, 2022
Title Hdac1_WT_late_2cell_rep2
Sample type SRA
 
Source name embryo
Organism Mus musculus
Characteristics tissue: embryo
developmental stage: late 2-cell
age: 36h after fertilization
treatment: embryos were injected with Hdac1 WT mRNA at zygote stage
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated from embryos using Picopure RNA isolation kit (Life Technologies, Grand Island, NY, USA) according to the manufacturer's instruction.
mRNAs were separated with oligo(dT)25 beads, and was used to prepare sequencing libraries with NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, mRNA was fragmented and reverse transcribed. The cDNA library was subject to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description fpkm_mouse.txt
Data processing Reads were trimmed by Trimmomatic to remove the bases with low quality and adapter sequences.
The trimmed reads were align to GRCm38 or ARS-UCD1.2 by Hisat2.
The raw reads counts of all expressed genes were quantified by FeatureCounts.
The abundance of all expressed genes were normalized to FPKM by Cufflinks.
Differentially expressed genes were selected by DESeq2 with Padj. <0.05 and fold change (FC) of >2 or <0.5.
Genome_build: GRCm38, ARS-UCD1.2
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM calculated by Cufflinks for each sample.
 
Submission date Aug 22, 2021
Last update date May 21, 2022
Contact name Kun Zhang
E-mail(s) kzhang@zju.edu.cn
Organization name Zhejiang University
Street address 866 Yuhangtang Rd
City Hangzhou
ZIP/Postal code 310058
Country China
 
Platform ID GPL24247
Series (2)
GSE182553 HDAC1/2 is indispensable for mouse and bovine ZGA via regulating distribution of H3K27ac and H3K4me3 [RNA-seq]
GSE182555 HDAC1/2 is indispensable for mouse and bovine ZGA via regulating distribution of H3K27ac and H3K4me3
Relations
BioSample SAMN20926151
SRA SRX11859089

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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