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Sample GSM3929481 Query DataSets for GSM3929481
Status Public on Mar 16, 2020
Title Arcuate nucleus, Phf6_ChIP_Fed_condition
Sample type SRA
 
Source name Arcuate nucleus
Organism Mus musculus
Characteristics strain: C57BL/6
age: 6-7 weeks
genotype: wild type
feeding condition: Fed
tissue: Arcuate nucleus
chip antibody: Phf6 (Sigma Aldrich, HPA001023)
Growth protocol Enriched ARC tissue dissected within 3 hours from 100 fed and 100 fasted wild-type mice (6-7 weeks old)
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and PHF6-chromatin complexes were isolated with PHF6 antibody.
Libraries were prepared following the NEB/NEBNext® Library Quant Kit for Illumina®(E7630S). Amplified libraries were size-selected using a 2% gel to capture fragments between 200 bp and 500 bp.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description Phf6_ChIPSeq_Fed_condition_FoldEnrichment.bw
Data processing ChIPseq reads were mapped to the mouse reference genome (GRCm38/mm10, downloaded from UCSC, http://genome.ucsc.edu/) using Bowtie 2 (version 2.2.9) with the following parameters: --local –X 2000.
Significant peaks were called using MACS2 (version 2.1.1.20160309) with “-f BAMPE” option and default threshold of q value (BH-adjusted p value) cutoff at 0.05.
The bedgrap file containing the signal ratio of ChIP to Input samples was acquired using MACS2 WITH “bdgcmp -m FE” option.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig file containing the signal ratio of ChIP to input.
 
Submission date Jul 06, 2019
Last update date Mar 16, 2020
Contact name Qian Li
E-mail(s) liqian@shsmu.edu.cn
Organization name Shanghai Jiao Tong University School of Medicine
Department Department of Anatomy and Physiology
Street address 280 South Chongqing Road, Building No.5, Room 408
City Shanghai
ZIP/Postal code 200025
Country China
 
Platform ID GPL17021
Series (2)
GSE133901 Chromatin binding protein PHF6 regulates activity-dependent transcription networks to promote hunger response [ChIP-Seq]
GSE139545 Chromatin binding protein PHF6 regulates activity-dependent transcription networks to promote hunger response
Relations
BioSample SAMN12226125
SRA SRX6410184

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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