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| Status |
Public on Mar 31, 2022 |
| Title |
RNA-seq-NC_rep2 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Bos taurus |
| Characteristics |
developmental stage: 8/16-cell
age: 3 day post insemination
treatment: embryos were injected with negative control siRNAs 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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| Data processing |
Reads were trimmed by Trimmomatic to remove the bases with low quality and adapter sequences
The trimmed reads were align to Bos_taurus_UMD_3.1.1 by Hisat2
The raw reads counts of all expressed genes were quatified by FeatureCounts
The abundance of all expressed genes were normalized to FPKM by Cufflinks
Genome_build: Bos_taurus_UMD_3.1.1
Supplementary_files_format_and_content: text file includes FPKM calculated by Cufflinks for each sample
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| Submission date |
Nov 18, 2021 |
| Last update date |
Mar 31, 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 |
GPL26012 |
| Series (2) |
| GSE189101 |
Genome-wide mapping of the histone modification H3K4me3 in bovine early embryos [RNA-seq] |
| GSE189102 |
Genome-wide mapping and gene expression of the histone modification H3K4me3 in bovine early embryos |
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| Relations |
| BioSample |
SAMN23282603 |
| SRA |
SRX13166060 |
| 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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