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Sample GSM4816111

Query DataSets for GSM4816111

Status

Public on Mar 24, 2021

Title

adipocyte WT rep2 (RNA-Seq)

Sample type

SRA

Source name

adipocytes

Organism

Mus musculus

Characteristics

strain: C57BL/6
tissue: epididymal adipose tissue
cell type: adipocytes
age: 17wks old
genotype: wild type

Extracted molecule

total RNA

Extraction protocol

Briefly, primary adipocytes were lysed for 1 h in lysis buffer at 37°C and digested with 10 g/mL proteinase K for 3 h at 50°C. After cell lysis, DNA and RNA was isolated by phenol-chloroform extraction and using trizol, respectively.
For WGBS library construction, 100ng of genomic DNA was treated with the EZ DNA Methylation-Gold kit (Zymo Research, Orange, CA, USA) for bisulfite conversion. Then, the sequencing libraries were prepared according to the manufacturer’s instructions of TruSeq DNA Methylation Library Preparation Kits (Illumina, #EGMK91396). Briefly, bisulfite-converted DNA is random-primed using a polymerase to synthesize DNA containing a specific sequence tag. The 3’ ends of the newly synthesized DNA strands are tagged with a second specific sequence. The di-tagged DNA molecules are amplified using FailSafe PCR Enzyme (Epicentre, #FSE51100) and TruSeq Index PCR Primer. The final purified product is quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using the Agilent Technologies 2100 Bioanalyzer (Agilent). Finally, sequencing was performed using the HiSeqX platform (Illumina). In case of RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

Adipocyte_FPKM_value.xlsx
AD5

Data processing

For WGBS data, sequenced reads were trimmed with adaptor sequences and performed quality control using TrimGalore v0.5.0. Then, the trimmed reads were mapped to the mouse genome (GRCm38) using Bismark v0.22.1. Cytosines that were mapped less than five reads were discarded for downstream analyses. Methylation levels of individual CpGs were determined using Bismark Methylation Extractor.
For RNA-seq data, Sequenced reads of adipocytes were trimmed with adaptor sequences and performed quality control by using trim galore. The trimmed reads were mapped to the mouse genome (GRCm38) using Rsubread v2.0.1. Raw read counts per genes were measured using featurecounts program in Rsubread with the builid-in mouse genome annotation (GRCm38).
Genome_build: mm10
Supplementary_files_format_and_content: wig files include CpG methylation values for each sample
Supplementary_files_format_and_content: Excel file include FPKM values for every genes and every adipocyte WT replicates.

Submission date

Oct 02, 2020

Last update date

Mar 24, 2021

Contact name

Yoon Jeong Park

Organization name

Seoul National University

Street address

San 56-1, Sillim-Dong, Gwanak-Gu

City

Seoul