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Sample GSM864674 Query DataSets for GSM864674
Status Public on Jan 31, 2012
Title RXR ChIP WT Control
Sample type SRA
Source name C57BL/6 wild type mouse liver
Organism Mus musculus
Characteristics strain: C57BL/6
gender: female
genotype/variation: wild type
treatment: Control
tissue: liver
antibody catalog #: SC-553
antibody vendor/provider: Santa Cruz
Treatment protocol Female C57BL/6 wild-type and LXRα/β-deficient mice (13 weeks of age) were treated by oral gavage once daily for 14 days with the RXR agonist bexarotene (100 mg/kg body weight [mpk], in 1% carboxymethylcellulose), the LXR agonist T0901317 (T09, 30 mpk) or vehicle alone.
Extracted molecule genomic DNA
Extraction protocol Chromatin was prepared from snap frozen livers, homogenized in PBS and cross-linked in 1% formaldehyde (10 min, RT). Cross-linked material was added 1M glycine to a final concentration of 0.125 M and incubated for 10 min rotating at RT, pelleted by centrifugation at 400xg for 2 min at 4°C, washed 2x in cold PBS and resuspended in lysis buffer (1% triton, 0.1% SDS, 150 mM NaCl, 2 mM EDTA, 1 mM EGTA, 20 mM Tris, pH 8.0) (200 μl/10 mg chromatin) before sonication according to the manufacturer’s protocol using the Diagenode Bioruptor twin (2x20 cycles, 30 sec. on/off, max. level). Samples were centrifuged for 2 min at 10.000xg and supernatant used for subsequent chromatin IP performed according to standard protocol. ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4 with the parameters -subpeaks 0.1 and -trim-peaks 0.3. All peaks with less than 10 overlapping reads were discarded.
Genome Build:
RXR_WT_Control.bed: mm9
RXR_WT_Control_peaks.bed: mm9
Submission date Jan 23, 2012
Last update date May 15, 2019
Contact name Susanne Mandrup
Phone +45 6550 2340
Organization name University of Southern Denmark
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense M
ZIP/Postal code 5230
Country Denmark
Platform ID GPL11002
Series (1)
GSE35262 Genome-wide profiling of LXR, RXR and PPARα in mouse liver reveals extensive sharing of binding sites
SRA SRX118176
BioSample SAMN00779753

Supplementary file Size Download File type/resource
GSM864674_RXR_WT_Control.bed.gz 31.8 Mb (ftp)(http) BED
GSM864674_RXR_WT_Control_peaks.bed.gz 143.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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