|
| Status |
Public on Apr 20, 2022 |
| Title |
RRBS D0 Control rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Abdominal preadipocyte cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: Control
differentiation time: D0
|
| Treatment protocol |
For adipogenesis, immortalized preadipocytes were cultured in growth medium first. Then, two days after full confluence (differentiation day 0), the cells were treated with adipogenic differentiation medium for 14 days. The differentiation medium is growth medium with Troglitazone (4 μM) and 3-isobutyl-1-methylxanthine (0.25 mM)
|
| Growth protocol |
Preadipocytes were cultured in Dulbecco's modified Eagle's medium/F12 Ham's nutrient mixture (v/v, 1:1) containing 17.5 mM glucose and supplemented with 10% foetal calf serum, 0.25 ng/ml fibroblast growth factor, 2 mM glutamine, 100 units/ml penicillin and 100 µg/ml streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RRBS: Genomic DNA was extracted using the GenEluteTM Mammalian Genomic DNA Miniprep Kit (Sigma)
RRBS libraries were constructed using Ovation® RRBS Methyl-Seq with TrueMethyl® oxBS preparation kit.
RNA-Seq: Use poly-T oligo-attached beads to purify and fragment mRNA for cDNA synthesis.
Then, a single ‘A’ nucleotide was added to 3’ end of ds cDNA, multiple indexing adaptors were ligated to 5’ and 3’ of the ends of ds cDNA, following with PCR amplification,
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
NextSeq 1000 |
| |
|
| Data processing |
BS-seq reads were trimmed (removing sequencing adapter and low-quality reads) by using Trimmomatic.
BS-seq reads were aligned to the human genome hg19 using BS-Seeker2, and in each read, at most 4 bp mismatches will be allowed. If multiple alignments mapped to the same location only one is kept.
Calling methylation levels and removing BS-seq reads with incomplete bisulfite conversion (#(mCH sites)/#(all CH sites)>0.8 and #(mCH sites)>5 for one read) by using BS-Seeker2.
The RNA-seq reads were aligned using HISAT2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: Processed data (CGmap) is in text format. column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.
|
| |
|
| Submission date |
Oct 19, 2021 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Pao-Yang Chen |
| Organization name |
Academia Sinica
|
| Department |
Institute of Plant and Microbial Biology
|
| Lab |
Pao-Yang Chen
|
| Street address |
128 Sec. 2, Academia Rd, Nankang,
|
| City |
Taipei |
| ZIP/Postal code |
115 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL30882 |
| Series (1) |
| GSE186159 |
Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through the epigenetic remodelling of genome-wide DNA methylation and transcription |
|
| Relations |
| BioSample |
SAMN22416131 |
| SRA |
SRX12693825 |
