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| Status |
Public on Nov 11, 2020 |
| Title |
20m-3 |
| Sample type |
SRA |
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| Source name |
whole blood
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: F344
age (months): 20.63
Sex: male
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
500ul of whole blood was collected via retro-orbital bleedings into heparinized tubes, spun, and the plasma removed. Buffy coat and red blood cells were frozen at -80 degrees C until DNA extraction. Following proteinase K and RNAse A treatments, DNA was isolated from rat blood cells using QIAmp DNA Mini Kit following manufacturer’s instructions using a QIAcube automated device. DNA was eluted from columns in 200 µL of AE buffer, concentrated in 20 µL 10 mM Tris-HCl, pH 8.5, 0.1 mM EDTA using Genomic DNA Clean & Concentrator-10, and quantified using a Qubit 2.0.
100ng of DNA isolated from whole blood was digested with MspI restriction enzyme (NEB, Ipswich, MA, USA), carried out end-repair/adenylation (NEB) and ligation with TruSeq barcoded adapters (Illumina, San Diego, CA, USA). DNA fragments of size range 200-300bp were selected with SPRI magnetic beads (ABM, Richmond, BC, CA), followed by bisulfite treatment (Millipore, Billerica, MA, USA), and PCR amplification (Bioline, Taunton, MA, USA). Libraries were sequenced by multiplexing 8 libraries per lane on the Illumina HiSeq2500 sequencer, with 100bp single end reads.
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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 |
Reduced alignment index generated using BSSeeker2 v2.1.8 with the following parameters; --aligner=bowtie2 -r -l 40 -u 500 -c C-CGG
Trimmed fastq files aligned using BSSeeker2 v2.1.8 using the following parameters; --aligner=bowtie2 --bt2--end-to-end --bt2-p 16 -r --low=40 --up=500 -f bam
Methylation values were called for methylat from alignments using BSSeeker2 v2.1.8 using the default parameters;
Genome_build: rn6
Supplementary_files_format_and_content: CGmap methylation call files; tab separated text file; (1) chromosome (2) nucleotide on Watson (+) strand (3) position (4) context (CG/CHG/CHH) (5) dinucleotide-context (CA/CC/CG/CT) (6) methylation-level = #_of_C / (#_of_C + #_of_T) (7) #_of_C (8) = #_of_C + #_of_T (
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| Submission date |
Nov 09, 2020 |
| Last update date |
Nov 12, 2020 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
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| Department |
Laboratory of Genetics and Genomics
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| Lab |
Computational Biology & Genomics Core
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| Street address |
251 Bayview Blvd
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE161141 |
A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin-associated histone modifications |
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| Relations |
| BioSample |
SAMN16710742 |
| SRA |
SRX9463856 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4890228_92.CGmap.gz |
82.0 Mb |
(ftp)(http) |
CGMAP |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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