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| Status |
Public on Jan 31, 2024 |
| Title |
Methyl_seq_6A2 |
| Sample type |
SRA |
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| Source name |
RD-RD Male
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hypothalamus
strain: C57BL/6J
Sex: male
genotype: WT
treatment: RD (no treatment)
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| Treatment protocol |
For Dams, C57BL/6J mice were maintained on either 52% fat high sucrose diet TD.04059.PWD hypercaloric diet (HCD) or regular chow diet (RD) for 1 month prior to mating and were kept on this diet for the duration of pregnancy and lactation. For offspring, mice were placed on either HCD or RD at weaning time and maintained until they reached 3 months old.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
At 3 month age, mice were euthanized and hypothalamus was flash frozen on dry ice for DNA extraction.
Extracted DNA was used to perform whole epigenome methylation sequencing. Methyl-Seq library preparation was performed using the SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing (Agilent Technologies, USA) as described by the manufacturer’s protocol. Briefly, 3 ìg of DNA was sheared to fragments of 100-200 bp using a Covaris M220 instrument followed by end repair and adapter ligation. DNA fragments were then subjected to hybridization to the SureSelectXT Methyl-Seq Mouse Capture Library for 16 h (Agilent Technologies, USA). Hybridized products were purified by capture with streptavidin beads and then subjected to bisulfite conversion using the Zymo EZ-DNA Methylation-Gold kit (Zymo Resesarch, USA). Libraries were enriched by PCR amplification. Unique indexes were then ligated to the amplified libraries by PCR amplification. The quality of the libraries was determined after end repair, adapter ligation, and indexing by Agilent’s Bioanalyzer 2100 using a high sensitivity DNA kit, to verify that the library peak size fell within the range recommended by the manufacturer’s protocol. Quantification of the final libraries was performed using the Qubit dsDNA high sensitivity assay (ThermoFisher Scientific, USA). Sequencing was performed on Illumina’s NextSeq 500 instrument with pair-end 100 bp reads.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Paired-end fastq reads were aligned to mm9 using Bismark(v0.22.3).
Methylation counts were extracted, clustered, and tested for differentially methylated regions using DMRfinder(v0.3).
Assembly: mm9
Supplementary files format and content: Tab-delimited text file with methylation counts for each sample.
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| Submission date |
Sep 01, 2023 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Mona Elgazzaz |
| E-mail(s) |
[email protected]
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| Phone |
5043569905
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| Organization name |
LSUHSC
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| Department |
Cardiovascular Center
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| Lab |
Lazartigues
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| Street address |
533 Bolivar Street
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| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE242186 |
Maternal Western Diet Programs Cardiometabolic Dysfunction and Hypothalamic Inflammation via Epigenetic Mechanisms Predominantly in the Male Offspring [Methyl-seq] |
| GSE242189 |
Maternal Western Diet Programs Cardiometabolic Dysfunction and Hypothalamic Inflammation via Epigenetic Mechanisms Predominantly in the Male Offspring |
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| Relations |
| BioSample |
SAMN37233198 |
| SRA |
SRX21594047 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7754584_6A2.cov.gz |
58.9 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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