GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM5694588 Query DataSets for GSM5694588
Status Public on Mar 31, 2022
Title RNA-seq-NC_rep2
Sample type SRA
Source name embryo
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
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
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
Submission date Nov 18, 2021
Last update date Mar 31, 2022
Contact name Kun Zhang
Organization name Zhejiang University
Street address 866 Yuhangtang Rd
City Hangzhou
ZIP/Postal code 310058
Country China
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
BioSample SAMN23282603
SRA SRX13166060

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap