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| Status |
Public on Aug 17, 2016 |
| Title |
Zr1087_1 |
| Sample type |
SRA |
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| Source name |
Achilles tendons
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
group: Un-Injured
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| 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
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| 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 (www.illumina.com). 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.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 1500 |
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| 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 (http://www.bioinformatics.babraham.ac.uk/projects/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.
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| Submission date |
Apr 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Katie J Trella |
| E-mail(s) |
trellakj@gmail.com
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| Organization name |
Rush University Medical Center
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| Department |
Orthopedics
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| Lab |
Sports Medicine
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| Street address |
1611 W. Harrison St, Suite 401A
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN04867730 |
| SRA |
SRX1711742 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2125941_zr1087_1_CpG_meth.bb |
56.7 Mb |
(ftp)(http) |
BB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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