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Sample GSM400660 Query DataSets for GSM400660
Status Public on May 12, 2009
Title L3_H3K4Me3_ChIPSeq_1
Sample type SRA
 
Source name L3
Organism Drosophila melanogaster
Characteristics tissue: L3
antibody: H3K4me3
antibody manufacturer: Abcam
antibody catalog number: ab8580
antibody lot number: 411277
Treatment protocol No Treatment
Growth protocol 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of third instar larvae (L3), new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Plates are then kept at 25C for another 48 hours. 3. L3 larvae are collected at 8.45 am using a filter mesh and a brush. L3 larvae are the larvae not going through the first mesh. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.
Extracted molecule genomic DNA
Extraction protocol Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description H3K4Me3_ChIPSeq_1
corresponding input record: GSM400661
Data processing Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).
 
Submission date May 07, 2009
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 GPL9058
Series (2)
GSE15292 Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-seq
GSE16013 Genome-wide maps of chromatin state in staged Drosophila embryos, ChIP-seq
Relations
SRA SRX013007
BioSample SAMN00005156
Named Annotation GSM400660_L3_H3K4Me3_Input_tag36_mfold4_250_peaks.bed.gz

Supplementary file Size Download File type/resource
GSM400660_L3_H3K4Me3_Input_tag36_mfold4_250_peaks.bed.gz 43.0 Kb (ftp)(http) BED
GSM400660_L3_H3K4Me3_run2_density.bedgraph.gz 20.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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