 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 17, 2018 |
| Title |
NMR_Bis_PCR_3 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Heterocephalus glaber |
| Characteristics |
tissue: Liver
age (wks): 910
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Targeted bisulfite PCR-based analysis was performed using the 48.48 layout on the Fluidigm C1 system (Fluidigm, USA), coupled with Illumina NextSeq sequencing. Bisulfite PCR primers were designed using Primer3 (PMID:17485472),
DNA was bisfulite converted (EpiTect, Qiagen) prior to amplification. Amplicons from a single sample were pooled and individually indexed to create a multiplex library prior to sequencing on an Illumina NextSeq instrument.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: Bis-PCR
Bismark (v0.13.1) was used to align reads to the reference genome camFam using Bowtie2
Methylation counts were extracted using https://bitbucket.org/lowelabqmul/methylation-extractor
Genome_build: hetGla2
Supplementary_files_format_and_content: chromsome,position,methylation count,total count
|
| |
|
| Submission date |
Sep 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Lowe |
| Organization name |
QMUL
|
| Department |
Blizard Institute
|
| Street address |
4 Newark Street
|
| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24046 |
| Series (2) |
| GSE86059 |
The rate of ageing-associated DNA methylation dynamics is a molecular readout of lifespan variation amongst mammalian species |
| GSE104215 |
The rate of ageing-associated DNA methylation dynamics is a molecular readout of lifespan variation amongst mammalian species [Bis-PCR: naked mole-rat] |
|
| Relations |
| BioSample |
SAMN07693481 |
| SRA |
SRX3213579 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2792667_3_counts.txt.gz |
1.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
