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Sample GSM3948917

Query DataSets for GSM3948917

Status

Public on Jul 19, 2019

Title

PLACT_7

Sample type

SRA

Source name

Placenta

Organism

Sus scrofa

Characteristics

tissue: Placenta
replicate: Rep7

Extracted molecule

total RNA

Extraction protocol

Total RNA were extrated by PAXgene RNA kit using the standard protocols.All samples were quantified using a NanoDrop 2000 (Thermo-Fisher Scientific, Waltham, MA, USA), and assessed with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA integrity number (RIN) of each sample was >8.
RNA libraries were prepared for sequencing using Super deepSAGE protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

Placenta

Data processing

Illumina Casava1.7 software used for basecalling.
RNA-Seq reads were mapped to pig reference mRNA (Sscrofa 10.2) using the SAGE data processiong software
Using R version 3.4.2 software to find differential genes
Clustering analysis was performed by first using K-means clustering method to separate the transcripts to several big groups, and then using Hierarchical clustering to build the internal structure of the transcripts within the groups according to method reported by Gu et al. (Gu et al. 2016).
The CLOVER software (Frith et al. 2004) with JASPAR PWM database (Khan et al. 2018) were used to identify over-represented transcription factor binding motifs for each cluster of genes.
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: Reads count (tab deli text)

Submission date

Jul 18, 2019

Last update date

Jul 19, 2019

Contact name

Tinghua Huang

E-mail(s)

thua45@yangtzeu.edu.cn

Phone

8613397215027

Organization name

Yangtze University