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Sample GSM463044 Query DataSets for GSM463044
Status Public on Jan 11, 2010
Title Drosophila-female-input-DNAseq
Sample type SRA
 
Source name ChIP input from Drosophila melanogaster adult female
Organism Drosophila melanogaster
Characteristics gender: female
antibody: none
Growth protocol Flies were grown at 25 °C on standard cornmeal media.
Extracted molecule genomic DNA
Extraction protocol Wild type flies (y1w67c) for chromatin immunoprecipitaion were aged for 5-7 days post-eclosion, sexed and flash frozen. About 0.5 g of sex-sorted adult flies was cross-linked with 1.8% for 20 minutes at room temperature. After washing, the flies were completely homogenized and the cells were disrupted by cell lysis and nuclei lysis. The nuclear extraction was then sheared to 200-1000bp by sonication using a Misonix Sonicator 3000 and the soluble chromatin was collected.
300 ng of DNA derived from sheared chromatin of female and male adult flies was prepared as ChIP input controls.
 
Library strategy OTHER
Library source genomic
Library selection RANDOM
Instrument model Illumina Genome Analyzer
 
Description DNA sequencing for chromatin structure
Data processing Image analysis and base calling were performed using a manufacturer-provided computational pipeline (version 0.3) including the Firecrest and Bustard applications and sequence reads were then aligned with the Drosophila melanogaster assembly (BDGP Release 5, dm3) using Bowtie (v 0.10.0). All unique mapped reads with two or fewer mismatches were retained.

Like DNase hypersensitivity assays, mechanically sheared chromatin breaks preferentially at some sites to provide information about chromatin structure genome-wide. Thus, we measured differential shearing accessibility in genome-wide experiments by deep DNA sequencing and increased mapped read density correlates with regions of preferential shearing. We are particularly interested in shearing and chromatin structure at gene models and different gene features to detect chromatin alternations associated with transcription.
Detailed analysis is included in the accompanying publication.

File description for *_bowtiealign.txt processed data files: sequence reads mapped to unique portion of the genome with two or fewer mismatches using Bowtie (v 0.10.0)
Column descriptions for *_bowtiealign.txt files:
Sequence: sequence of the aligned reads
Chromosome: chromosome reads mapped to
Location: chromosomal position where alignment starts
Strand: forward or reverse strand the reads mapped to
 
Submission date Oct 20, 2009
Last update date May 15, 2019
Contact name Brian Oliver
E-mail(s) briano@nih.gov
Phone 301-204-9463
Organization name NIDDK, NIH
Department LBG
Lab Developmental Genomics
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL9058
Series (1)
GSE15593 Sex-dependent and -independent X-chromosome histone modifications in Drosophila melanogaster
Relations
SRA SRX016014
BioSample SAMN00008201

Supplementary file Size Download File type/resource
GSM463044_input-female_bowtiealign.txt.gz 42.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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