|
| Status |
Public on Jan 25, 2016 |
| Title |
roX ChIRP-seq in four Drosophila species |
| Organisms |
Drosophila melanogaster; Drosophila virilis; Drosophila willistoni; Drosophila busckii |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We identified orthologs of the roX lncRNAs across diverse Drosophilid species, and then mapped the genomic binding sites of roX1 and roX2 in four Drosophila species (D. melanogaster, D. willistoni, D. virilis, and D. busckii) using ChIRP-seq (chromatin isolation by RNA Purification and sequencing), thus revealing the interplay of the evolution of roX1 and roX2 and their genomic binding sites.
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| |
|
| Overall design |
We found roX1 and roX2 orthologs in D. willistoni, D. virilis, and D.busckii and designed antisense biotinylated 20-mer ChIRP oligos against each RNA target. The ChIRP oligo pools were then divided into Even (E) or Odd (O) pools for independent ChIRP experiments for each RNA target. In each species, chromatin was prepared directly from larval tissue; the RNA target was recovered using the indicated ChIRP oligo pools. Input DNA was sampled from the prepared chromatin. DNA from each ChIRP-seq experiment was purified, prepared into libraries, and sequenced as described. Each sample was then mapped to the respective Drosophila genome; each even-odd pair was then merged and peaks were called using MACS2.
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| |
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| Contributor(s) |
Quinn JJ, Zhang QC, Chang HY |
| Citation(s) |
26773003 |
| Submission date |
May 26, 2015 |
| 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 |
| |
|
| Platforms (5)
|
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
| GPL20239 |
Illumina NextSeq 500 (Drosophila willistoni) |
| GPL20240 |
Illumina NextSeq 500 (Drosophila virilis) |
| GPL20241 |
Illumina NextSeq 500 (Drosophila busckii) |
|
| Samples (35)
|
| GSM1695366 |
D.melanogaster roX2 (Odd) ChIRP-seq |
| GSM1695367 |
D.melanogaster input DNA |
| GSM1695368 |
D.willistoni roX1 (Even) ChIRP-seq |
| GSM1695369 |
D.willistoni roX1 (Odd) ChIRP-seq |
| GSM1695370 |
D.willistoni roX2/3 (Even) ChIRP-seq |
| GSM1695371 |
D.willistoni roX2/3 (Odd) ChIRP-seq |
| GSM1695372 |
D.willistoni input DNA |
| GSM1695373 |
D.virilis roX1 (Even) ChIRP-seq |
| GSM1695374 |
D.virilis roX1 (Odd) ChIRP-seq |
| GSM1695375 |
D.virilis roX2 (Even) ChIRP-seq |
| GSM1695376 |
D.virilis roX2 (Odd) ChIRP-seq |
| GSM1695377 |
D.virilis input DNA |
| GSM1695378 |
D.busckii roX1 (Even) ChIRP-seq |
| GSM1695379 |
D.busckii roX1 (Odd) ChIRP-seq |
| GSM1695380 |
D.busckii roX2 (Even) ChIRP-seq |
| GSM1695381 |
D.busckii roX2 (Odd) ChIRP-seq |
| GSM1695382 |
D.busckii input DNA |
| GSM1974906 |
D.busckii roX2 (Even) ChIRP-seq (with transgenic D.busckii roX2) |
| GSM1974907 |
D.busckii roX2 (Odd) ChIRP-seq (with transgenic D.busckii roX2) |
| GSM1974908 |
D.melanogaster input DNA (with transgenic D.busckii roX2) |
| GSM1974909 |
D.melanogaster roX1 (Even) ChIRP-seq (with transgenic D.melanogaster roX1) |
| GSM1974910 |
D.melanogaster roX1 (Odd) ChIRP-seq (with transgenic D.melanogaster roX1) |
| GSM1974911 |
D.melanogaster input DNA (with transgenic D.melanogaster roX1) |
| GSM1974912 |
D.melanogaster roX2 (Even) ChIRP-seq (with transgenic D.melanogaster roX2) |
| GSM1974913 |
D.melanogaster roX2 (Odd) ChIRP-seq (with transgenic D.melanogaster roX2) |
| GSM1974914 |
D.melanogaster input DNA (with transgenic D.melanogaster roX2) |
| GSM1974915 |
D.melanogaster roX2-mutated (Even) ChIRP-seq (with transgenic D.melanogaster roX2 with mutated stem-loops) |
| GSM1974916 |
D.melanogaster roX2-mutated (Odd) ChIRP-seq (with transgenic D.melanogaster roX2 with mutated stem-loops) |
| GSM1974917 |
D.melanogaster input DNA (with transgenic D.melanogaster roX2 with mutated stem-loops) |
| GSM1974918 |
D.virilis roX1 (Even) ChIRP-seq (with transgenic D.virilis roX1) |
| GSM1974919 |
D.virilis roX1 (Odd) ChIRP-seq (with transgenic D.virilis roX1) |
| GSM1974920 |
D.melanogaster input DNA (with transgenic D.virilis roX1) |
|
| Relations |
| BioProject |
PRJNA284887 |
| SRA |
SRP058701 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE69208_BUS-roX1.merge.bedGraph.gz |
34.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_BUS-roX1.merge.bw |
201.5 Mb |
(ftp)(http) |
BW |
| GSE69208_BUS-roX2.merge.bedGraph.gz |
81.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_BUS-roX2.merge.bw |
277.4 Mb |
(ftp)(http) |
BW |
| GSE69208_Dbus.269_peaks-500bp.bed.gz |
2.4 Kb |
(ftp)(http) |
BED |
| GSE69208_Dbus_genome_assembly.fa.gz |
36.9 Mb |
(ftp)(http) |
FA |
| GSE69208_Dbus_protein_annotation.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE69208_Dmel.293_peaks-500bp.bed.gz |
2.5 Kb |
(ftp)(http) |
BED |
| GSE69208_Dvir.309_peaks-500bp.bed.gz |
2.8 Kb |
(ftp)(http) |
BED |
| GSE69208_Dwil.528_peaks-500bp.bed.gz |
5.0 Kb |
(ftp)(http) |
BED |
| GSE69208_MEL-roX1.merge.bedGraph.gz |
7.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_MEL-roX1.merge.bw |
32.6 Mb |
(ftp)(http) |
BW |
| GSE69208_MEL-roX2.merge.bedGraph.gz |
7.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_MEL-roX2.merge.bw |
30.7 Mb |
(ftp)(http) |
BW |
| GSE69208_Muller_Element_Assignments.xlsx.gz |
264.8 Kb |
(ftp)(http) |
XLSX |
| GSE69208_RAW.tar |
2.4 Gb |
(http)(custom) |
TAR (of BEDGRAPH, BW) |
| GSE69208_Trans-BUS-roX2-input.bedGraph.gz |
100.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_Trans-BUS-roX2-input.bw.gz |
73.0 Mb |
(ftp)(http) |
BW |
| GSE69208_Trans-BUS-roX2-merge.bedGraph.gz |
14.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_Trans-BUS-roX2-merge.bw.gz |
55.9 Mb |
(ftp)(http) |
BW |
| GSE69208_Trans-MEL-roX1-input.bedGraph.gz |
107.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_Trans-MEL-roX1-input.bw.gz |
76.8 Mb |
(ftp)(http) |
BW |
| GSE69208_Trans-MEL-roX1-merge.bedGraph.gz |
18.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_Trans-MEL-roX1-merge.bw.gz |
54.1 Mb |
(ftp)(http) |
BW |
| GSE69208_Trans-MEL-roX2-input.bedGraph.gz |
104.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_Trans-MEL-roX2-input.bw.gz |
75.1 Mb |
(ftp)(http) |
BW |
| GSE69208_Trans-MEL-roX2-merge.bedGraph.gz |
31.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_Trans-MEL-roX2-merge.bw.gz |
85.6 Mb |
(ftp)(http) |
BW |
| GSE69208_Trans-MEL-roX2mut-input.bedGraph.gz |
102.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_Trans-MEL-roX2mut-input.bw.gz |
74.4 Mb |
(ftp)(http) |
BW |
| GSE69208_Trans-MEL-roX2mut-merge.bedGraph.gz |
8.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_Trans-MEL-roX2mut-merge.bw.gz |
48.1 Mb |
(ftp)(http) |
BW |
| GSE69208_Trans-VIR-roX1-input.bedGraph.gz |
104.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_Trans-VIR-roX1-input.bw.gz |
75.9 Mb |
(ftp)(http) |
BW |
| GSE69208_Trans-VIR-roX1-merge.bedGraph.gz |
3.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_Trans-VIR-roX1-merge.bw.gz |
10.1 Mb |
(ftp)(http) |
BW |
| GSE69208_VIR-roX1.merge.bedGraph.gz |
54.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_VIR-roX1.merge.bw |
260.5 Mb |
(ftp)(http) |
BW |
| GSE69208_VIR-roX2.merge.bedGraph.gz |
114.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_VIR-roX2.merge.bw |
305.9 Mb |
(ftp)(http) |
BW |
| GSE69208_WIL-roX1.merge.bedGraph.gz |
43.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_WIL-roX1.merge.bw |
252.3 Mb |
(ftp)(http) |
BW |
| GSE69208_WIL-roX2.merge.bedGraph.gz |
105.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE69208_WIL-roX2.merge.bw |
292.6 Mb |
(ftp)(http) |
BW |
| GSE69208_roX1s.rtf.gz |
24.0 Kb |
(ftp)(http) |
RTF |
| GSE69208_roX2s.rtf.gz |
10.9 Kb |
(ftp)(http) |
RTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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