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Status |
Public on May 21, 2022 |
Title |
Hdac1_WT_late_2cell_rep2 |
Sample type |
SRA |
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Source name |
embryo
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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
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
fpkm_mouse.txt
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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.
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Submission date |
Aug 22, 2021 |
Last update date |
May 21, 2022 |
Contact name |
Kun Zhang |
E-mail(s) |
kzhang@zju.edu.cn
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Organization name |
Zhejiang University
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Street address |
866 Yuhangtang Rd
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City |
Hangzhou |
ZIP/Postal code |
310058 |
Country |
China |
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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 |
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Relations |
BioSample |
SAMN20926151 |
SRA |
SRX11859089 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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