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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 03, 2024 |
| Title |
M00018001_15M_Lung_iPCRtag77 |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
strain: C57BL/6 J
age: 15M
genotype: wildtype
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from ~10 mg frozen tissue using the DNeasy Blood & Tissue Kit (Qiagen)
RRBS libraries were prepared from isolated DNA following published protocols (Stubbs et al 2017). Briefly, RRBS libraries were prepared by MspI digestion of 100–500 ng genomic DNA, followed by end-repair and T-tailing using Klenow Exo- (Fermentas). Adapter ligation was performed overnight (in-house adapters) using T4 DNA Ligase (NEB), followed by a clean-up step using AMPure XP beads (Agencourt, 0.9×). Subsequently, libraries were bisulfite-treated according to the manufacturer’s instructions (Sigma Imprint Kit; 2 step protocol) and purified using an automated liquid handling robotic system (Agilent Bravo). The libraries were amplified using KAPA HiFi Uracil HotStart DNA Polymerase (KAPA Biosystems), indexing the samples with individual primers. All amplified libraries were purified (AMPure XP beads, 0.8×) and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer.
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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 |
RRBS and WGBS datasets were processed as described previously (RRBS: Stubbs et al., 2017; WGBS: von Meyenn, 2022), aligning reads to the bisulfite converted GRCm38 mouse genome using Bismark v0.22.3 (Krueger and Andrews, 2011).
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files are tab separated and contain DNA methylation data with the following columns: chromosome, start, end, methylation, methylated reads, nonmethylated reads.
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| Submission date |
Feb 13, 2023 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Laura Biggins |
| E-mail(s) |
laura.biggins@babraham.ac.uk
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| Organization name |
The Babraham Institute
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| Department |
Bioinformatics
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| Street address |
Babraham Research Campus
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| City |
Cambridge |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE225166 |
Predicting age in single cells and low coverage DNA methylation data [RRBS] |
| GSE225173 |
Predicting age in single cells and low coverage DNA methylation data |
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| Relations |
| BioSample |
SAMN33270149 |
| SRA |
SRX19352192 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7040598_lane8_GAGGTGCT_M00018001_15_M_Lung_iTAG_77_merged_L008_R1.barcode_removed_val_1_GRCm38_bismark_bt2_pe.deduplicated.bismark.cov.gz |
20.9 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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