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Sample GSM1500750 Query DataSets for GSM1500750
Status Public on Apr 29, 2015
Title Hif1a pulldown replicate 1
Sample type SRA
 
Source name embryonic heart
Organism Mus musculus
Characteristics developmental stage: E12.5
strain: Black-Swiss
genotype: Wild-type
antibody: anti-HIF1a
Extracted molecule genomic DNA
Extraction protocol E12.5 mouse hearts were dissected and cross-linked in 1.5% of formaldehyde methanol-free for 10 minutes at room temperature. Samples were quenched by incubation with 2.5M glycine for 5 minutes. Hearts were ressuspended in lysis buffer (50 mM HEPES-KOH pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP40; 0.25% Triton X-100) and dounce homogenized for nuclei isolation. The cross-linked chromatin was sonicated in Shearing buffer (1mM EDTA; 10mM Tris-HCl pH 7.6; 0.1% SDS) using a Covaris S2 (2% Duty cycle, 3 Intensity; 200 cycles per burst; for 8 minutes) to an average size of 200 bp. Precleared chromatin extract was incubated overnight at 4°C with 4μg of rabbit anti-HIF-1α antibody (Novus) and immunoprecipitated with protein A–Sepharose beads. 10 ng of ChIP DNA was used to generate a standard Illumina sequencing library.
libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Data processing Reads were mapped to mm10 genome build with Bowtie2
Homer software was used to make tag directory with default settings
Homer was used for peak calls using findPeaks function using cIP1/Input and cIP2/Input files separately using the -F 2 and -P .05 modifications to default
Peaks were merged with Homer's software MergePeaks function
Genome_build: Mm10
Supplementary_files_format_and_content: Data fields with Peak IDs and coordinates are saved as tab delimited .txt files
 
Submission date Sep 09, 2014
Last update date May 15, 2019
Contact name Alexander C Zambon
Organization name Keck Graduate Institute
Department Biopharmaceutical Sciences
Lab Zambon
Street address 517 Watson Drive
City Claremont
State/province CA
ZIP/Postal code 91711
Country USA
 
Platform ID GPL16417
Series (1)
GSE61247 ChIP-seq profiling of loci bound by HIF1a in wild-type E12.5 hearts
Relations
SRA SRX698168
BioSample SAMN03031484

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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