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| Status |
Public on May 03, 2017 |
| Title |
Condensin plays a role in both interphase nuclei and premature chromosome condensation |
| Organism |
Gallus gallus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: to identify how condensin I removal affects gene expression globally.
Methods: Chicken DT40 CAP-H KO cells were treated with or without dox for 36 h. Total RNA samples were extracted and subjected to sequencing using an Illumina Hiseq2000 platform. Library preparation and Illumina sequencing were performed by Macrogen (South Korea). The sequence tags were spliced-mapped onto the chicken genome galGal4 using Tophat and Bowtie2 following quality test using FASTQC. Differential expression of genes was analyzed using the Bioconductor v2.3 package edgeR v3.2.3. Tag enrichment in NCBI RefSeq genes was calculated between dox-treated and untreated cells using edgeR exact test with tag-wise dispersion estimation.
Results: We identified a total of 3798 genes to be differentially expressed in G1 condensin I-depleted chicken DT40 cells: 2495 down regulated and 1303 up regulated.
Conclusions: Removal of CAP-H leads to significant misregulation of gene expression, suggesting a key role for condensin I in transcription during interphase.
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| Overall design |
Total RNA profiles of CAP-H KO cells with or without Dox were generated by sequencing using Illumina Hiseq2000 platform.
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| Contributor(s) |
Zhang T, Hudson D, Kim JH |
| Citation(s) |
27008552 |
| |
| Submission date |
Nov 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao Zhang |
| Organization name |
Murdoch childrens research institute
|
| Department |
Chromosome Research
|
| Street address |
Flemington Road, Parkville
|
| City |
Melbourne |
| State/province |
Vic |
| ZIP/Postal code |
3502 |
| Country |
Australia |
| |
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| Platforms (1) |
| GPL16133 |
Illumina HiSeq 2000 (Gallus gallus) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA301739 |
| SRA |
SRP066020 |
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