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Sample GSM4889183

Query DataSets for GSM4889183

Status

Public on Mar 16, 2021

Title

oocyte sirt6-2

Sample type

SRA

Source name

porcine oocyte

Organism

Sus scrofa

Characteristics

tissue: oocyte
development stage: Metaphase II
group: sirt6 inhibited

Extracted molecule

total RNA

Extraction protocol

The cell was lysised and the RNA was amplificated according to Smart-seq2 procedures.
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Data processing

All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.13)
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized using cuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: susScr11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

Submission date

Nov 09, 2020

Last update date

Mar 16, 2021

Contact name

Li Yu

E-mail(s)

2018105031@njau.edu.cn

Organization name

College of Animal Science and Technology, Nanjing Agricultural University

Street address

No. 1 Weigang, Nanjing City, Jiangsu Province