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Sample GSM945887 Query DataSets for GSM945887
Status Public on Feb 07, 2013
Title Yki embryo ChIP, replicate3
Sample type SRA
 
Source name 8-16hr embryo ChIP; Iso1 strain; Yki antibody
Organism Drosophila melanogaster
Characteristics strain: Iso1
developmental stage: Embryo, 8-16hr
tissue: Whole embryo
antibody: anti-Yki
Growth protocol Embryos were collected at 8-16 hours after egg laying. For wing discs, wandering 3rd instar larvae were manually removed from Drosophila culture. Larvae were inverted in PBS to expose imaginal discs. Imaginal discs dissected off before fixation.
Extracted molecule genomic DNA
Extraction protocol Chromatin lysates were clarified from homogenized and sonicated tissues; protein-DNA complexes were isolated with antibody. DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911). Briefly, up to 12.5 ng DNA was included in the high molecular weight (HMW) tagmentation reaction (5 minutes at 55 degrees Celsius). Tagmented DNA was purified using a Qiagen MinElute column. Addition of barcoded PCR-compatible sites and library enrichment were performed using 12 cycles of PCR. Amplified DNA was purified using the Qiagen MinElute PCR Purification Kit. Library fragments of approximately 225 bp were gel purified and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a HiSeq2000 according to the manufacturer’s protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Yki embryo ChIP, replicate 3
Yki_E8-16.bedGraph
Yki_E8-16.bed
Data processing The Raw images were first processed with the Casava 1.7.0.
Base-called sequences with confidence metrics were obtained using OLB-1.9.0.  All multiplexed samples were demultiplexed using Casava 1.7.0
The BWA program was used to align the sequence reads to the Drosophila melanogaster (v5.32) genome, allowing up to 2 edit distance in the seed region and 3 in the full read length. Tags that aligned to more than one  location were excluded from our analysis for both ChIP sample and the corresponding control sample (input chromatin). Only properly aligned reads with mapping quality more than 30 were kept.
Peaks were called using MACS (v2), on merged replicates, using bandwidth of 100 and a p-value cutoff of 1E-5
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files were generated using SPP from sorted bam file, which was generated by SAM/bowtie, under 100 bp step
 
Submission date Jun 08, 2012
Last update date May 15, 2019
Contact name Kevin P. White
E-mail(s) kpwhite@uchicago.edu
Organization name University of Chicago
Department Institute for Genomics and Systems Biology
Street address 900 E. 57th STR. 10th FL.
City Chicago
State/province IL
ZIP/Postal code 60615
Country USA
 
Platform ID GPL13304
Series (2)
GSE38594 Genome-wide binding of Yki and GAF in embryos and wing imaginal discs [ChIP-Seq]
GSE43130 Genome-wide binding of Yki and GAF in embryos and wing imaginal discs
Relations
SRA SRX152095
BioSample SAMN01041475

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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