|
| Status |
Public on Aug 01, 2015 |
| Title |
ChIP input |
| Sample type |
SRA |
| |
|
| Source name |
mK4
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
cell line: mK4
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
SpDamID used Dneasy extraction kit, DpnI digestion, and ligation mediated PCR to generate libraries that are in turn sonicated and ligated to bar-coded Illumina sequencing adaptors; FAIRE was performed by sonicating formaldehyde cross-linked nuclei and phenol:chloroform extraction of open chromatin compared to input DNA extracted after cross-link reversal, ChIP used myc-epitope tag to immunoprecipitate bound DNA from sonicated cross-linked DNA
Illumina library construction protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Illumina next-generation sequencing
|
| Data processing |
SpDamID-seq enriched segments were identified using Poisson model comparing against DAM library and for the triplicates only segments called in 2 out of 3 replicates were retained
N1 ChIP enriched segments were identified by requiring over 10 fold more reads than in the input and segments mapping to repeat regions were masked
Total FAIRE sites were identified using MAC peak calling of N1wt FAIRE compared against input and requiring that the same site must be present in all 3 N1wt vs input FAIRE comparisons
Notch1-dependent FAIRE sites were identified using MAC peak calling of N1wt FAIRE compared against Control FAIRE and requiring that the same site must have been called in all 3 N1wt vs Control FAIRE comparisons
Genome_build: mm9
|
| |
|
| Submission date |
Jun 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Raphael Kopan |
| E-mail(s) |
rafi.kopan@cchmc.org
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Developmental Biology
|
| Lab |
Kopan
|
| Street address |
3333 Burnet Avenue
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE70387 |
SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers [next-generation sequencing] |
| GSE70402 |
SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers |
|
| Relations |
| BioSample |
SAMN03801556 |
| SRA |
SRX1077229 |
