|
| Status |
Public on Jan 25, 2016 |
| Title |
D.melanogaster roX2-mutated (Even) ChIRP-seq (with transgenic D.melanogaster roX2 with mutated stem-loops) |
| Sample type |
SRA |
| |
|
| Source name |
D.melanogaster mixed-sex wandering 3rd instar larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole larvae
developmental stage: third instar larval stage
gender: mixed
|
| Growth protocol |
Larvae were raised at room temperature on standard cornmeal molasses or Wheeler-Clayton medium. Larvae were collected at wander third instar larval stage.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from recovered chromatin fraction by ChIRP by gentle elution with Rnase A and H, proteinase K digestion, and phenol-chloroform extraction.
ChIRP-seq libraries were prepared using NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina with standard TruSeq adapters.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Trans-MEL-roX2mut-merge.bedGraph
Trans-MEL-roX2mut-merge.bw
|
| Data processing |
Data processing was performed following the ChIRP-seq pipeline (Chue et al., 2011). Reads were trimmed for adaptor sequence, mapped using bowtie to the respective Drosophila spp. genome, and Even and Odd pairs were merged. ChIRP-seq peaks were called using MACS2.
Fastq > bedGraph > bigWig
Genome_build: multiple: melanogaster = dm3, willistoni = dwil_r1.3, virilis = dvir-all-r1.2, busckii = Dbus_genome_assembly.fa; see Supplementary Information
Supplementary_files_format_and_content: Processed merged and input ChIRP-seq tracks (bedGraph and bigWig)
Supplementary_files_format_and_content: Called ChIRP-seq peaks (roX binding sites; bed format)
Supplementary_files_format_and_content: Genome assembly (fasta format) and genome annotation (bed format) are included for D.busckii
Supplementary_files_format_and_content: Müller element (chromosome arm) assignments for genome assemblies are included for all species
Supplementary_files_format_and_content: all roX1 and roX2 sequences used in this analysis are included in text format
|
| |
|
| Submission date |
Dec 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
[email protected]
|
| 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 |
GPL19132 |
| Series (1) |
| GSE69208 |
roX ChIRP-seq in four Drosophila species |
|
| Relations |
| BioSample |
SAMN04349921 |
| SRA |
SRX1490788 |
