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Sample GSM977025 Query DataSets for GSM977025
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) jaiganesha@gmail.com
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

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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