 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 19, 2021 |
| Title |
G68 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Heterocephalus glaber |
| Characteristics |
age (years): 1.72
gender: Male
breeding status: Non-breeder
colony: 2-Jul
lab: Vera Gorbunova
date of collection: 2019-10-10
tissue: Blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
To collect blood, animals were placed headfirst into a plastic restraining cone (decapicone, Braintree Scientific) such that the tail remained accessible outside of the cone. The tail was then positioned on a benchtop, ventral side up. A sterile razor blade was used to make a superficial incision across the ventral surface of the tail about halfway between the body and end of the tail. The incision induced bleeding from the tail vein. The animal was then positioned above a blood collection tube (BD Microtainer, tubes with K2EDTA, Becton, Dickinson and Company) so that blood drops from the incision were collected into the collection tube. The collected blood was immediately snap-frozen. After the blood collection, gentle pressure was applied to the tail incision site for one to two minutes to stop further bleeding. The blood DNA was extracted by DNeasy Blood & Tissue Kit (Qiagen 69506) and cleaned up using RNase treatment followed by concentration. The DNA was eluted from Qiagen columns in 100 µl of 10 mM Tris-HCl buffer, pH 8.0. RNA removal was performed with 2 µl of RNase A (Life Technologies) at room temperature for 2 minutes and isolated genomic DNA was purified using Genomic DNA Clean & Concentrator™-10 (Zymo D4011), 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 from 100 ng of purified DNA per sample following a protocol described in Petkovich et al. 2017. The libraries were sequenced with Illumina HiSeq2500, PE150. 20% of PhiX genomic DNA was spiked to compensate for the low complexity of the libraries.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
G68_CKDL190142107-1a-27_H5YNKBBXX_L6
|
| Data processing |
Reads were trimmed and quality filtered by TrimGalore! using the --rrbs option for RRBS.
Methylation levels were extracted using Bismark with Bowtie 2 mapping to the NMR genome (HetGla_female_1.0).
As the number of contigs exceeded the maximum allowed to be used in mapping, we concatenated short contigs (less than 1,000,000 bp) into a pseudocontig separated by 1,000 ‘N’.
For further analysis, we used only the CpG sites that are covered by at least 5 reads in at least 90% of the samples.
Genome_build: HetGla_female_1.0
Supplementary_files_format_and_content: Bismark coverage (cov) files containing read coverage and methylation level of each CpG site
|
| |
|
| Submission date |
Jun 28, 2021 |
| Last update date |
Dec 20, 2021 |
| Contact name |
Vadim N. Gladyshev |
| E-mail(s) |
vgladyshev@rics.bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital and Harvard Medical School
|
| Department |
Department of Medicine
|
| Lab |
Gladyshev Lab
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21195 |
| Series (1) |
| GSE179039 |
Epigenetic aging of the demographically non-aging naked mole-rat [RRBS] |
|
| Relations |
| BioSample |
SAMN19918374 |
| SRA |
SRX11243346 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5404308_G68_CKDL190142107-1a-27_H5YNKBBXX_L6_1_val_1_bismark_bt2_pe.bismark.cov.gz |
41.4 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
