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| Status |
Public on May 11, 2012 |
| Title |
high fat diet |
| Sample type |
SRA |
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| Source name |
quadriceps muscle
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: 15 weeks
tissue: quadriceps muscle
treatment: LF
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| Treatment protocol |
Mice were placed on respective diets at 5 weeks of age and maintained in thermoneutral conditions with ad libitum water and food for 10 weeks before euthanization and muscle extraction.
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| Growth protocol |
Mice were purchased from Jackson laboratories at 4 weeks of age and subsequently housed in Comparative Biology at the Pennington Biomedical Research Center in thermoneutral conditions (22-23°C) with ad libitum water and food.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
After 10 wks on their respective diets, mice were euthanized and quadriceps muscle was excised and snap frozen in liquid nitrogen. Due to the homogeneity of the tissue, quadriceps muscle was ground under liquid nitrogen with a motor and pestle to create a homogenous sample. 50mg of powdered tissue was then used to isolate nuclei via dounce homogenization in a 0.25M sucrose buffer (0.25M sucrose, in 10mM Tris-acetate, 1mM EDTA, 1mM DTT, 1mM sodium orthovanadate and a 1X protease inhibitor tablet) on ice. Isolated nuclei were resuspended in digestion buffer (0.25M sucrose buffer plus 4mM MgCl2 and 1mM CaC2) and incubated at 37°C with MNase for 15 min (90-95% partial digestion), as previously described. Native chromatin without cross-linking was released from nuclei by incubation a lysis buffer containing 50mM Tris, 10mM EDTA, 1% SDS and a protease inhibitor cocktail. Mononucleosomal DNA was collected and pooled from 5 mice per treatment group. Mononucleosomal and a control undigested genomic DNA were purified by EtOH precipitation after an overnight digestion with 0.1mg/mL of protease K at 37°C. For DNA sequencing, nucleosomal DNA was further modified following the SOLiD sequencing protocol and sequenced with a SOLiD 5500xl Genetic Analyzer (Applied Biosystems).
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
AB 5500xl Genetic Analyzer |
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| Data processing |
Basecalls were performed using 5500 Series Genetic Analyzers Instrument Control Software v1.2.
Reads were trimmed for the adaptor sequence and aligned to the UCSC mm9 genome using Bowtie version 0.12.7 with the following parameters: - n 2 -l 28 - e 40.
Peaks were called using HOMER software using the following parameters: -fdr 0.05 -size 147 -minDist 162 -tagThreshold 4 -L 0 -C 0 -F 0 -o (read count ≥4; false discovery rate = 0.05; peak size = 147; minimum distance between peaks = 162; genome size = 2,000,000,000; number of tags used for normalization = 10,000,000; size of region used for local filtering = 10,000; Poisson p-value over local region = 1.00e-04).
Genome_build: mm9
Supplementary_files_format_and_content: fasta and qual files were generated using 5500 Series Genetic Analyzers Instrument Control Software v1.2 and are formatted as such: (column 1), (column 2), (column 3). Text files were generated from HOMER and are formatted as follows: PeakID (column 1), chromosome (column 2), start index (column 3), end index (column 4), strand (column 5), peak score (column 6), focus ratio/region size (column 7), annotation (column 8), detailed annotation (column 9), distance to transcription start site (column 10), nearest promoter ID (column 11), Entrez ID (column 12), nearest Unigene (column 13), nearest Refseq (column 14), nearest Ensembl (column 15), gene name (column 16), gene alias (column 17), gene description (column 18), CpG% (column 19), GC% (column 20).
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| Submission date |
May 10, 2012 |
| Last update date |
Mar 07, 2024 |
| Contact name |
Tara M Henagan |
| Organization name |
Louisiana State University Health Sciences Center - Shreveport
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| Department |
Medical School
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| Street address |
1501 Kings Hwy
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| City |
Shreveport |
| State/province |
LA |
| ZIP/Postal code |
71103 |
| Country |
USA |
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| Platform ID |
GPL15907 |
| Series (1) |
| GSE37913 |
Nucleosome maps in skeletal muscle in response to diet in vivo |
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| Relations |
| SRA |
SRX147716 |
| BioSample |
SAMN00993175 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM929893_outfile_annotated_HFpeaks4_05.txt.gz |
518.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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