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Sample GSM4805472

Query DataSets for GSM4805472

Status

Public on Jan 31, 2021

Title

NOTCH1_KD rep1

Sample type

SRA

Source name

embryo

Organism

Bos taurus

Characteristics

tissue: embryo
developmental stage: Late morula (D6 after IVF)
knockdown: NOTCH1

Extracted molecule

polyA RNA

Extraction protocol

Total RNA extraction was performed using Picopure RNA isolation kit (Life Technologies, Grand Island, NY, USA) based on the manufacturer's manual. Before RNA isolation, equal amount of GFP and RFP mRNA were added to each group as a spike-in control.
mRNAs separation was achieved using oligo(dT)25 beads. Sequencing libraries were constructed with NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the instruction. In brief, mRNAs were fragmented followed by reverse transcription. The cDNA library underwent end repair, poly(A)-tailing, adaptor ligation, and PCR amplification for 12–15 cycles to prepare sequencing libraries.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Data processing

Reads were trimmed to remove the bases with low quality and adapter sequences
The trimmed reads were assigned directly to transcripts and counted with Salmon software
Gene expression level was quantified and normolized by Salmon(v0.14.1)
Differentially expressed genes between NC and KD group were selected by DESeq2
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Text files include normalized counts by DESeq2 for each sample

Submission date

Sep 28, 2020

Last update date

Jan 31, 2021

Contact name

Kun Zhang

E-mail(s)

kzhang@zju.edu.cn

Organization name

Zhejiang University

Street address

866 Yuhangtang Rd