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| Status |
Public on May 12, 2022 |
| Title |
Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [ChIP-seq] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
While Drosophila has widespread contact domains, most domain boundaries are formed independently of CTCF by unclear mechanisms. We genetically ablate the ubiquitous boundary-associated factor Cp190 and examine impacts on genome folding and developmental gene regulation in Drosophila embryos. We find that Cp190 is widely required to form fly domain boundaries that are distal from transcribed gene promoters, while promoter proximal boundaries are unaffected by Cp190 loss.
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| Overall design |
Chromatin was prepared from 0-14 hour old embryos that were wildtype, Cp190[0], CTCF[0] or double[0] (i.e. CTCF[0] and Cp190[0]), in biological triplicates. Chromatin was also prepared from wildtype (WT), Cp190[KO] and su(Hw)[KO] mutant third instar larval central nervous systems (CNSs) in biological duplicates. ChIP-seq was performed with antibodies recognizing CTCF or Cp190. Multiplexed ChIP-seq libraries were sequenced paired-end on 2 (for embryo ChIP) or 1 (for larval CNS ChIP) lanes of a HiSeq4000 instrument.
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| Contributor(s) |
Kaushal A, Dorier J, Wang B, Cousin P, Taschner M, Mohana G, Omer A, Semenova A, Iseli C, Waridel P, Quadroni M, Guex N, Aiden EL, Gambetta MC |
| Citation(s) |
35559678 |
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| Submission date |
Jul 19, 2021 |
| Last update date |
Jun 01, 2022 |
| Contact name |
Maria Cristina Gambetta |
| E-mail(s) |
mariacristina.gambetta@unil.ch
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| Organization name |
University of Lausanne
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| Department |
Center for Integrative Genomics
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| Street address |
Genopode Building
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL21306 |
Illumina HiSeq 4000 (Drosophila melanogaster) |
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| Samples (23)
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| GSM5461672 |
Cp190 ChIP, CTCF[0], rep1 |
| GSM5461673 |
Cp190 ChIP, CTCF[0], rep2 |
| GSM5461674 |
Cp190 ChIP, CTCF[0], rep3 |
| GSM5461675 |
Cp190 ChIP, WT[0], rep1 |
| GSM5461676 |
Cp190 ChIP, WT[0], rep2 |
| GSM5461677 |
Cp190 ChIP, WT[0], rep3 |
| GSM5461678 |
CTCF ChIP, Cp190[0], rep2 |
| GSM5461679 |
CTCF ChIP, Cp190[0], rep3 |
| GSM5461680 |
CTCF ChIP, CTCF[0], rep1 |
| GSM5461681 |
CTCF ChIP, CTCF[0], rep2 |
| GSM5461682 |
CTCF ChIP, CTCF[0], rep3 |
| GSM5461683 |
CTCF ChIP, WT[0], rep1 |
| GSM5461684 |
CTCF ChIP, WT[0], rep2 |
| GSM5461685 |
CTCF ChIP, WT[0], rep3 |
| GSM5461686 |
Cp190 ChIP, WT larval CNS, rep1 |
| GSM5461687 |
Cp190 ChIP, WT larval CNS, rep2 |
| GSM5461688 |
Cp190 ChIP, Cp190[KO] larval CNS, rep1 |
| GSM5461689 |
Cp190 ChIP, Cp190[KO] larval CNS, rep2 |
| GSM5461690 |
Cp190 ChIP, su(Hw)[KO] larval CNS, rep1 |
| GSM5461691 |
Cp190 ChIP, su(Hw)[KO] larval CNS, rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE180376 |
Essential role of Cp190 in physical and regulatory boundary formation in Drosophila |
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| Relations |
| BioProject |
PRJNA748171 |
| SRA |
SRP329151 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE180374_RAW.tar |
2.9 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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