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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 01, 2023 |
| Title |
MYC_SOL_1 |
| Sample type |
SRA |
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| Source name |
soleus
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| Organism |
Mus musculus |
| Characteristics |
tissue: Skeletal Muscle
conditions: Myc overexpression
age: 2.5mo
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| Treatment protocol |
Soleus tissue and DNA were extracted and reduced representation bisulfite sequencing (RRBS) for whole-genome and ribosomal DNA-specific analysis.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from the soleus tissue using the Quick-DNA™ Miniprep Plus kit (Zymo Research, D4068) as specified in the protocol.
“Classic” RRBS library preparation was performed by digesting genomic DNA with 30 units of MspI enzyme (New England BioLabs, R0106), and fragments were ligated to pre-annealed adapters containing 5’-methyl-cyotosine. Adapter-ligated fragments ≥50 base pairs were recovered using the DNA Clean & Concentrator Kit (Zymo Research, D4003) and bisulfite-converted using the EZ DNA Methylation-Lightning KitTM (Zymo Research, D5030) following the standard protocol. Preparative-scale PCR was performed, and the products were purified again using the Clean and Concentrator kit.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Base calling with Illumina Software
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore
The effect of trimming and overall quality distribution was determined using FastQC
Alignment was performed using Bismark
Read totals were called using Bismark Methylation Extractor
Assembly: A custom genome assembly to interrogate both nuclear and rDNA methylation was generated by adding the consensus rDNA repeat sequences, BK000964.3, as a separate chromosome to the GRCm39 (GCA_000001635.9) mouse reference genome assembly.
Supplementary files format and content: Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome
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| Submission date |
Jan 06, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Kevin Murach |
| E-mail(s) |
kmurach@uark.edu
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| Organization name |
University of Arkansas
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| Department |
Health, Human Performance, and Recreation
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| Lab |
Molecular Muscle Mass Regulation Laboratory
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| Street address |
155 Stadium Dr.
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| City |
Fayetteville |
| State/province |
AR |
| ZIP/Postal code |
72701 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE222330 |
A Molecular Signature Defining Exercise Adaptation and In Vivo Reprogramming in Skeletal Muscle [BiSulfite-seq] |
| GSE222335 |
A Molecular Signature Defining Exercise Adaptation and In Vivo Reprogramming in Skeletal Muscle |
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| Relations |
| BioSample |
SAMN32617894 |
| SRA |
SRX18955404 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6920877_zr7806_11_S709_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz |
25.9 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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