|
| Status |
Public on Jun 18, 2012 |
| Title |
L(3)mbt_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
Kc cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
chip antibody: L(3)mbt
cell type: Kc167 Drosophila Embryonic Cell line
|
| 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 |
Chromatin IP against L(3)mbt
|
| 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.
Genome Build:
L3mbt.bed: DM3
L3mbt.wig: DM3
|
| |
|
| Submission date |
Mar 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Van Bortle |
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Michael Snyder
|
| Street address |
3165 Porter Dr
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94043 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE36393 |
Distribution of Drosophila insulator proteins Mod(mdg4) and L(3)mbt in Kc cells |
|
| Relations |
| SRA |
SRX128327 |
| BioSample |
SAMN00810072 |
