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| Status |
Public on Apr 21, 2023 |
| Title |
DNA from liver from YoungIsoRec3 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
mouse strain: C57BL/6 WT
tissue: liver
age (years): 0.666666667
mouseid: YoungIsoRec3
condition: Young isochronic recovery
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| Treatment protocol |
Parabiosis was carried out as previously described (Zhang et al., 2021). Female C57Bl/6 mice were pre-screened to minimize body size differences, and were randomly assigned to parabiosis pairs. Isochronic pairs consisted of two 3-month-old mice and heterochronic pairs consisted of one 3-month-old mouse and one 20-month-old mouse. Pairs were surgically attached and maintained for 3 months. Following 3 months of parabiosis, a subset of mice were euthanized for analysis and another subset were surgically separated. Fascia and skin were sutured closed following separation, and mice were allowed to recover for 2 months, after which they were for euthanized for analysis.
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| Growth protocol |
This experiment was approved by the Duke University IACUC. C57Bl/6 mice were obtained from Jackson Laboratories and acclimated to our animal facility for at least 48 h before being subjected to any experimental manipulation. Aged C57Bl/6 mice for parabiosis experiments were obtained from the NIA aged rodent colony. Mice were maintained in a barrier facility in sterilized, ventilated cages and fed standard laboratory chow (LabDiet 5053) and reverse osmosis drinking water ad libitum and maintained on a 12h:12h light:dark cycle. Mice were generally housed socially. Mice were humanely euthanized at the conclusion of each experiment by CO2 exposure followed by cervical dislocation.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from samples was isolated by using the DNeasy Blood & Tissue Kit (Qiagen 69506), and then eluted from columns in 100 μl of 10 mM TrisHCl buffer, pH 8.0. 2 μl of RNase A (Life Technologies) was added to each sample. Samples were incubated at room temperature for 2 min, and isolated genomic DNA was purified by using the Genomic DNA Clean & Concentrator™-10 kit (Zymo D4011). DNA was eluted in 25 μl of 10 mM Tris-HCl buffer, pH 8.0 and quantified using a Qubit 2.0 (Life Technologies AM2271).
RRBS libraries were prepared following the protocol previously established (Petkovich et al., 2017), using 100 ng of DNA for each sample. Each library included 10 samples. To avoid an overlap of batch effect and age-related changes, we randomized samples across libraries. The libraries were sequenced using an Illumina HiSeq2500, with 150bp paired-end reads. 20% of mouse genomic DNA library was spiked in to compensate for low complexity of the libraries.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Adapter removal and quality trimming for the analysis of DNA methylation reads were performed using TrimGalore v0.4.1 following previously established protocols (Krueger and Andrews, 2011; Meer et al., 2018; Petkovich et al., 2017)
Trimmed reads were mapped to the mouse genome (GRCm38.p2/mm10) using Bismark v0.15.0. (Krueger and Andrews, 2011)
Coverage files outputted by Bismark were then used for further analyses.
Assembly: mm10
Supplementary files format and content: Bismark .cov files with methylation calls and coverage for each locus
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| Submission date |
Feb 03, 2023 |
| Last update date |
Apr 21, 2023 |
| Contact name |
Jesse Poganik |
| Organization name |
Brigham and Women's Hospital, Harvard Medical School
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| Department |
Medicine/Genetics
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE224442 |
DNA methylation changes in mice induced by parabiosis and recovery [RRBS] |
| GSE224447 |
DNA methylation and gene expression changes in mice induced by parabiosis and recovery |
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| Relations |
| BioSample |
SAMN33053298 |
| SRA |
SRX19274326 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7022439_BZ23_CKDL200159088-1a-6_HC7TWCCX2_L4_1_val_1.fq.gz_bismark_bt2_pe.bismark.cov.gz |
29.1 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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