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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 28, 2017 |
| Title |
Lung_27wk_M0112371 |
| Sample type |
SRA |
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| Source name |
Lung_27wk
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| Organism |
Mus musculus |
| Characteristics |
age: 27wk
tissue: Lung
strain: C57BL/6 BABR
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
All tissues were snap frozen directly after isolation. Genomic DNA was isolated from ~10mg frozen tissue using the DNeasy Blood & Tissue Kit (Qiagen).
RRBS libraries were prepared from isolated DNA following published protocols (Smallwood et al.,2011). Briefly, RRBS libraries were prepared by MspI digestion of 100-500ng genomic DNA, followed by end-repair and T-tailing using Klenow Exo- (Fermentas). Adapter ligation was performed overnight (homemade adapters) using T4 DNA Ligase (NEB), followed by a cleanup step using AMPure XP beads (Agencourt, 0.9x). Subsequently, libraries were bisulfite treated according to the manufactures 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, 0.8x) and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer. High-throughput sequencing of all libraries was carried out with a 75 bp paired-end protocol on a HiSeq 2000 instrument (Illumina).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
RRBS and ChIP-BS-Seq: Trimmed sequences were mapped to the mouse GRCm38 genome using Bismark (Krueger and Andrews, 2011) (v0.16.3); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts. For details, see Stubbs et al.
Genome_build: GRCm38
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>
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| Submission date |
Jan 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Felix Krueger |
| E-mail(s) |
fkrueger@altoslabs.com
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| Organization name |
Altos Labs
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| Department |
Bioinformatics
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| Street address |
Granta Park
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| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE93957 |
Multi-tissue DNA methylation age predictor in mouse |
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| Relations |
| Reanalyzed by |
GSE120136 |
| BioSample |
SAMN06250808 |
| SRA |
SRX2511254 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2465646_M0112371_27wk_Lung.cov.txt.gz |
22.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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