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Sample GSM2125941 Query DataSets for GSM2125941
Status Public on Aug 17, 2016
Title Zr1087_1
Sample type SRA
Source name Achilles tendons
Organism Mus musculus
Characteristics strain: C57BL/6
group: Un-Injured
Treatment protocol Chronic Achilles tendinopathy was induced via two injections of TGF-β1 directly into the body of the tendon. Mice were then sacrificed on day 3 or underwent normal cage activity or treadmill running for 14 or 28 days
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared from 200-500 ng of genomic DNA (from 5-6 tendons) digested with 60 units of TaqαI and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research (ZR) DNA Clean & Concentrator™-5 kit (Cat#: D4003)
Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines ( Adaptor-ligated fragments of 150–250 bp and 250–350 bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (Zymoclean™ Gel DNA Recovery Kit, ZR Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (ZR, Cat#: D5020).
Preparative-scale PCR was performed and the resulting products were purified (DNA Clean & Concentrator™ - ZR, Cat#D4005) for sequencing on an Illumina HiSeq.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 1500
Data processing Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software and then analyzed using a Zymo Research proprietary analysis pipeline, which is written in Python and used Bismark ( to perform the alignment
Index files were constructed using the bismark_genome_preparation command and the entire reference genome. The --non_directional parameter was applied while running Bismark. All other parameters were set to default.
Filled-in nucleotides were trimmed off when doing methylation calling. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Fisher’s exact test or t-test was performed for each CpG site which has at least five reads coverage, and promoter, gene body and CpG island annotations were added for each CpG included in the comparison.
For post-processing, CpG sites with methylation differentials greater than 80% (0.8) for any experimental group relative to UI were used.
Submission date Apr 18, 2016
Last update date May 15, 2019
Contact name Katie J Trella
Organization name Rush University Medical Center
Department Orthopedics
Lab Sports Medicine
Street address 1611 W. Harrison St, Suite 401A
City Chicago
State/province IL
ZIP/Postal code 60612
Country USA
Platform ID GPL18480
Series (1)
GSE80396 Genome-wide alterations in DNA methylation identify Leprel2, Foxf1, Mmp25, Igfbp6 and Peg12 as disease-associated genes in murine Achilles tendinopathy 
BioSample SAMN04867730
SRA SRX1711742

Supplementary file Size Download File type/resource 56.7 Mb (ftp)(http) BB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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