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Sample GSM1958884 Query DataSets for GSM1958884
Status Public on Aug 10, 2016
Title Cre Input ChIP-Seq
Sample type SRA
 
Source name Input DNA for Cre sample
Organism Mus musculus
Characteristics strain: C57Bl/6
cell type: Chondrocytes
genotype/variation: hdac3-knockout
transduction: Cre-recombinase adenovirus
chip antibody: None
Treatment protocol NA
Growth protocol NA
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Libraries were prepared according to NuGene Ultralow library prep kit V2
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Primary mouse chondrocytes, cultured ex vivo in micromass cultures, transduced with Cre-recombinase adenovirus
Data processing bcl2fastq v1.8.4 is used for basecalling
Data was processed with Mayo chip-seq pipeline-- HiChIP (http://www.biomedcentral.com/1471-2105/15/280).
Paired_end reads are aligned to genome with BWA. Duplicated reads are filtered out with picard. Peak calling is performed with Sicer
Genome_build: mm10
Supplementary_files_format_and_content: This file contains a list of peaks, from left to right are: chr, start, end, peak ID, integer score for display, fold-change, -log10pvalue, -log10qvalue and peak summit position relative to peak start
 
Submission date Dec 01, 2015
Last update date May 15, 2019
Contact name Jennifer Jane Westendorf
E-mail(s) Westendorf.Jennifer@mayo.edu
Organization name Mayo Clinic
Street address 200 First Street SW
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
 
Platform ID GPL13112
Series (2)
GSE75547 Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes[ChIP-Seq]
GSE75552 Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes
Relations
BioSample SAMN04304506
SRA SRX1457513

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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