|
| Status |
Public on May 01, 2013 |
| Title |
DREF_Mitosis_ChIPseq_1 |
| Sample type |
SRA |
| |
|
| Source name |
Kc167
|
| Organism |
Drosophila melanogaster |
| Characteristics |
chip antibody: DREF Rabbit polyclonal
cell line: Kc167
cell type: Embryonic Cell
|
| Growth protocol |
Kc cells were maintained in HyClone CCM3 Serum-free media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200–1000 bp DNA fragments. Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC. Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC. After washing and eluting from beads the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’ - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
DREF_Mitosis_ChIPseq_1
*these were ChIP-seq experiments, and not paired for data analysis
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples and a p-value cutoff of 1e-10.
The paired-end files were treated independently, thus, the raw files have been brokered/processed as single-end.
|
| |
|
| Submission date |
Jul 26, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gurudatta Baraka Vishwanathan |
| E-mail(s) |
[email protected]
|
| Phone |
404 727 4250
|
| Organization name |
Emory University
|
| Department |
Biology Department
|
| Lab |
Victor Corces
|
| Street address |
1510 clifton road ne
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE39664 |
Distribution of Drosophila insulator proteins DREF in Drosophila Kc167 cells |
|
| Relations |
| SRA |
SRX170985 |
| BioSample |
SAMN01095610 |
