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Sample GSM3942595

Query DataSets for GSM3942595

Status

Public on Sep 30, 2021

Title

F-L rep2

Sample type

SRA

Source name

epididymal WAT

Organism

Mus musculus

Characteristics

strain: C57BL/6
tissue: epididymal WAT
age: 35-week-old
genotype: wild type

Treatment protocol

C57BL/6 mice were fed with high fat diet (HF) (60% kcal fat; Research Diets Inc., New Brunswick, NJ) or low fat diet (LF) (10% kcal fat; Research Diets Inc.) at 6-week-old. Nine weeks after in HF, a part of mice was switched to LF for one week followed by one week HF as one cycle, and the mice under this one week diet switch protocol for 10 cycles were named HF-LF cycled mice, while the left part of mice under continuously HF-feeding were named HF mice. The mice kept in the continuously LF-feeding were named LF mice

Growth protocol

C57BL/6 breeding pairs were housed at a controlled temperature with a 12 hr/12 hr light/dark cycle, with free access to water and food. Animals were handled according to the Guidelines of the China Animal Welfare Legislation and approved by the Committee on Ethics in the Care and Use of Laboratory Animals of College of Life Sciences, Wuhan University.

Extracted molecule

total RNA

Extraction protocol

Total RNA from each sample was extracted using Trizol reagent (Life Technologies), and concentration was measured using an ND-1000 NanoDrop (Thermo Scientific, Wilmington, DE). RNA integrity was evaluated using the Agilent 2200 Tape Station (Agilent Technologies, Santa Cruz Biotechnology), and samples with an RNA integrity value above 7.0 were used. RNA-Seq was performed at RiboBio Co., Ltd. (Guangzhou, China) using the HiSeq 2500 platform (Illumina, San Diego, CA). Prior to sequencing, raw data were filtered to produce high-quality clean data, and all subsequent analyses were performed using clean data.
Briefly, mRNAs were isolated from total RNA, fragmented to approximately 200 bp, and subjected to first strand and second strand cDNA synthesis followed by adaptor ligation and low-cycle enrichment according to the instructions of the TruSeq RNA LT/HT Sample Prep Kit (Illumina, San Diego, CA, USA). Purified library products were evaluated using the Agilent 2200 Tape Station and Qubit 2.0 software (Life Technologies)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.1.0 with default parameters. The number of reads mapped to each gene was calculated by Htseq.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

Submission date

Jul 16, 2019

Last update date

Sep 30, 2021

Contact name

Yu Sun

E-mail(s)

1225194625@qq.com

Phone

18707192719

Organization name

Wuhan University