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Sample GSM6547529

Query DataSets for GSM6547529

Status

Public on Jun 30, 2023

Title

Liver_PC-AR_T31_rep3

Sample type

SRA

Source name

Liver

Organism

Rattus norvegicus

Characteristics

tissue: Liver
group: Model
treatment: PC-AR

Treatment protocol

In the treatment phase, the rats in control group (0.9% saline) were fed with normal diet and the rat model were continuously supplied with HFD but regrouped into three groups according to different administration solution: model group (0.9% saline), 12.6g/kg HTJZD group and 4.54g/kg PC-AR group for 4 weeks. Each rat was given an intragastric dose of 1 mL/100g.

Growth protocol

Before treatment, the rat model of HLP was established by the fed with high-fat diet for 4 weeks.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from liver tissue samples by using TRIzol reagent.
The cDNA library was constructed following the manufacturer’s instructions of NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, E7530）and NEB Next Multiplex Oligos for Illumina ( NEB, E7500). In briefly, the enriched mRNA was fragmented into approximately 200nt RNA inserts, which were used to synthesize the first-strand cDNA and the second cDNA. The double-stranded cDNA were performed end-repair/dA-tail and adaptor ligation. The suitable fragments were isolated by Agencourt AMPure XP beads (Beckman Coulter, Inc.), and enriched by PCR amplification. Finally, the constructed cDNA libraries of the honey bee were sequenced on a flow cell using an Illumina HiSeq™ sequencing platform.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

PC-AR_rep3_T31

Data processing

Low quality reads, such as only adaptor, unknown nucleotides>5%, or Q20 <20% (percentage of sequences with sequencing error rates <1%), were removed by perl script.
The clean reads that were filtered from the raw reads were mapped to honeybee (Apis mellifera) genome (OGSv3.2) using Tophat2 (Kim, Pertea et al. 2013) software.
The aligned records from the aligners in BAM/SAM format were further examined to remove potential duplicate molecules.
Gene expression levels were estimated using FPKM values (fragments per kilobase of exon per million fragments mapped) by the Cufflinks software (Trapnell, Williams et al. 2010).
Assembly: Rnor_6.0_release85
Supplementary files format and content: tab-delimited text file include RPKM values for 16 Samples

Submission date

Sep 06, 2022

Last update date

Jun 30, 2023

Contact name

Xiaowen Zhou

E-mail(s)

drawen@163.com, 20191101004@stu.gzucm.edu.cn

Organization name

Guangzhou University of Chinese Medicine

Street address

No.232, East Waihuan Road, Guangzhou Higher Education Mega Centre, Panyu District