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Sample GSM1280467 Query DataSets for GSM1280467
Status Public on Jun 16, 2014
Title LacZ_control
Sample type SRA
 
Source name male third instar larval dorsal mesothoracic disc
Organism Drosophila melanogaster
Characteristics tissue: dorsal mesothoracic disc
strain: CME W1 cl.8+
strain: third instar larva
Sex: male
chirp-seq target: LacZ control
Treatment protocol Harvested cells were crosslinked with 1% glutaraldehyde or 1+3% formaldehyde following Chu et al. 2011 and Simon et al. 2011
Growth protocol Cells were cultured according to cell line maintenance protocol from the Drosophila Genome Resource Center (dgrc.cgb.indiana.edu)
Extracted molecule genomic DNA
Extraction protocol Purified DNA was extracted by gentle RNase elution and Qiagen column purification
For sequencing libraries we followed Illumina’s protocol.
Purification protocol: Following the ChIRP protocol in Chu et al., 2011, biotinylated DNA oligos antisense to the target RNA were added to crosslinked, sonicated chromatin for target hybridization. Biotinylated ChIRP oligos, RNA target, and associated chromatin/DNA were purified on streptavidin-functionalized magnetic beads. For ChIRP-seq, the recovered DNA was extracted from each sample.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description library strategy: ChIRP-Seq
Data processing Raw reads were uniquely mapped to Drosophila melanogaster reference genome (dm3 assembly) using bowtie (version 0.12.6) allowing maximum one mismatch
Even-Odd sequencing pairs were normalized for number of reads and merged, following Chu et al. 2011
Peaks for each sample were called using MACS algorithm (version 1.4.2) and summits were identified by ZINBA
Genome_build: dm3
Supplementary_files_format_and_content: processed ChIRP genomic tracks are in .bw format
Supplementary_files_format_and_content: called peaks are in .bed format
 
Submission date Dec 05, 2013
Last update date May 15, 2019
Contact name Kun Qu
E-mail(s) kqu@stanford.edu
Organization name Stanford University
Department Dermatology
Lab Howard Chang
Street address 269 Campus Dr. CCSR 2150
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL13304
Series (1)
GSE53020 Domain ChIRP reveals the modularity of long noncoding RNA architecture, function, and target genes
Relations
BioSample SAMN02437267
SRA SRX387585

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

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