NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1088967 Query DataSets for GSM1088967
Status Public on Sep 20, 2013
Title chico_chip_1
Sample type SRA
 
Source name female adult flies
Organism Drosophila melanogaster
Characteristics strain: chico heterozygous mutants
age: 15-day-old
chip antibody: dFOXO
gender: female
genotype: chico heterozygous mutants
tissue: whole organism
Extracted molecule genomic DNA
Extraction protocol About 200-250 adult females (~200 mg) at the age of 15-day-old were pooled for each ChIP sample. Flies were homogenized and cross-linked in 1 X PBS containing 1 % formaldehyde. The fly lysate were sonicated using Branson 450 sonicator to break down the chromatin into a pool of DNA fragment with average size of 500 bp. Immunoprecipitation was performed using Dynal protean A beads (Invitrogen) and affinity purified anti-dFOXO antibody made in our laboratory . Following the wash with LiCl and TE buffer, the DNA-protein complex was eluted from the Dynal beads, reverse-crosslinked and purified.
About 20 ng of ChIP DNA (dFOXO-bound DNA) and input DNA (DNA sample before the immunoprecipitation) were used in library preparation following the methods described in Quail, M.A., et al., Nat Methods. 2008 (5). 1005-1010. Briefly, DNA was end-repaired using an End-It DNA End Repair Kit from Epicentre (# ER0720). The blunt, phosphorylated ends were treated with Klenow (3’->5’ exo-) from NEB (# M0212s) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 150~350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing Basecalls performed using CASAVA version 1.6
ChIP-seq reads were aligned to the Drosophila reference genome (dmel5.22) using Bowtie
Reads from two replicates were pulled together before peak calling
Peaks were called using PeakSeq with the following setting:
min_threshold = 30 max_threshold = 100 max_gap = 100 number_of_sims = 5 FDR_required = 0.01 bin_size = 10000 max_count = 3 Pf=1 pval_threshold=0.01
Genome_build: dmel5.22
Supplementary_files_format_and_content: candi_final_with_gene.txt files were generated to show the nearest gene next to the candidate peaks
 
Submission date Feb 26, 2013
Last update date May 15, 2019
Contact name Hua Bai
E-mail(s) hua_bai@brown.edu
Organization name Brown University
Department EEB
Lab Marc Tatar Lab
Street address 34 Olive St, BMC502
City Providence
State/province RI
ZIP/Postal code 02912
Country USA
 
Platform ID GPL11203
Series (1)
GSE44686 Genome-wide analysis of dFOXO binding sites in Drosophila
Relations
SRA SRX245834
BioSample SAMN01925591

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap