|
| Status |
Public on Jun 16, 2014 |
| Title |
roX1_Even |
| 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: roX1
|
| 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 Genome Analyzer IIx |
| |
|
| 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 |
GPL11203 |
| Series (1) |
| GSE53020 |
Domain ChIRP reveals the modularity of long noncoding RNA architecture, function, and target genes |
|
| Relations |
| BioSample |
SAMN02437268 |
| SRA |
SRX387577 |
