|
| Status |
Public on Apr 29, 2015 |
| Title |
Hif1a pulldown replicate 2 |
| 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 |
SRX698169 |
| BioSample |
SAMN03031485 |
