|
| Status |
Public on Oct 03, 2017 |
| Title |
Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum |
| Organism |
Tribolium castaneum |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Evolution of cis-properties (such as enhancers) often plays an important role in the production of diverse morphology. However, a mechanistic understanding is often limited by the absence of methods to study enhancers in species outside of established model systems. Here, we sought to establish methods to identify and test enhancer activity in the red flour beetle, Tribolium castaneum. To identify possible enhancer regions, we first obtained genome-wide chromatin profiles from various tissues and stages of Tribolium via FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)-sequencing. Comparison of these profiles revealed a distinct set of open chromatin regions in each tissue and stage. Second, we established the first reporter assay system that works in both Drosophila and Tribolium, using nubbin in the wing and hunchback in the embryo as case studies. Together, these advances will be useful to study the evolution of cis-language and morphological diversity in Tribolium and other insects.
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|
| Overall design |
Open chromatin profiling by FAIRE-seq during Tribolium development: 3 stages of embryogenesis (2-replicates each); larval CNS(2-replicates); larval second and third thoracic segments (3-replicates each); Genomic DNA Inputs. Sequencing performed on Illumina HiSeq 2000.
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| |
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| Contributor(s) |
Lai Y, Deem KD, Borras-Castells F, Sambrani N, Rudolf H, Suryamohan K, El-Sherif E, Halfon MS, McKay DJ, Tomoyasu Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Oct 02, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Yoshinori Tomoyasu |
| E-mail(s) |
tomoyay@miamioh.edu
|
| Phone |
513-529-3126
|
| Organization name |
Miami University
|
| Department |
Biology
|
| Street address |
700E High St
|
| City |
Oxford |
| State/province |
Ohio |
| ZIP/Postal code |
45056 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL18255 |
Illumina HiSeq 2000 (Tribolium castaneum) |
|
| Samples (16)
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| Relations |
| BioProject |
PRJNA412867 |
| SRA |
SRP119255 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE104495_0hr_FAIRE_merged_q10.bw.gz |
7.0 Mb |
(ftp)(http) |
BW |
| GSE104495_24hr_FAIRE_merged_q10.bw.gz |
5.0 Mb |
(ftp)(http) |
BW |
| GSE104495_48hr_FAIRE_merged_q10.bw.gz |
7.5 Mb |
(ftp)(http) |
BW |
| GSE104495_RAW.tar |
7.6 Mb |
(http)(custom) |
TAR (of NARROWPEAK) |
| GSE104495_larval_CNS_FAIRE_merged_q10.bw.gz |
12.3 Mb |
(ftp)(http) |
BW |
| GSE104495_larval_INPUT_merged_q10.bw.gz |
12.0 Mb |
(ftp)(http) |
BW |
| GSE104495_larval_T2_FAIRE_merged_q10.bw.gz |
9.3 Mb |
(ftp)(http) |
BW |
| GSE104495_larval_T3_FAIRE_merged_q10.bw.gz |
10.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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