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GEO help: Mouse over screen elements for information. |
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Status |
Public on Sep 02, 2020 |
Title |
Control_Diet_RXR_KO_1 |
Sample type |
SRA |
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Source name |
Knockout Mouse fed control diet for 12 weeks
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Organism |
Mus musculus |
Characteristics |
strain: C57BL6/J genotype: PPARg knockout gender: male age: 5 months tissue: liver treatment: Control Diet chip antibody: RXR antibody (sc-774 )
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Treatment protocol |
Mice were fed either control diet or high fat diet supplemented with Pio or vehicle.
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Extracted molecule |
genomic DNA |
Extraction protocol |
As described in Huang et al., Identification of an epigenetic signature of early mouse liver regeneration that is disrupted by Zn-HDAC inhibition, Epigenetics, 2015. PubMed: 25482284 As described in Huang et al., Identification of an epigenetic signature of early mouse liver regeneration that is disrupted by Zn-HDAC inhibition, Epigenetics, 2015. PubMed: 25482284
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 3000 |
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Data processing |
Basecalls performed using RTA Version 2.7.3 ChIP-seq reads were aligned to the mm10 genome assembly using novoalign version V3.04.06 with harclipping (-H) and adapter stripping (-a) Peaks were called using MACS version version 2.1.1 (20160309) using a paired input control Genome_build: mm10 Supplementary_files_format_and_content: Bed files: The bed files contain the called peaks, the 5th column is the standard MACS -10*log10pvalue; Xls files: contain the peaks with additional information, such as position of peak summit, number of tags in peak region, fold enrichment and FDR
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Submission date |
Sep 22, 2019 |
Last update date |
Sep 02, 2020 |
Contact name |
Paul Cliften |
E-mail(s) |
pcliften@wustl.edu
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Organization name |
Washington University
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Department |
Genetics
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Lab |
GTAC
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Street address |
4320 Forest Park Parkway
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City |
St. Louis |
ZIP/Postal code |
63108 |
Country |
USA |
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Platform ID |
GPL21493 |
Series (1) |
GSE137820 |
Pioglitazone induces extensive PPARg-dependent hepatic expression of nuclear-mitochondrial genes |
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Relations |
BioSample |
SAMN12816686 |
SRA |
SRX6886002 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4088990_1_control_rxr_minus_31_control_input_peaks.narrowPeak.gz |
255.8 Kb |
(ftp)(http) |
NARROWPEAK |
GSM4088990_1_control_rxr_minus_31_control_input_peaks.txt.gz |
297.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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