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| Status |
Public on Nov 14, 2014 |
| Title |
Genome-wide analysis of the RNA polyemerase I trascription factor UBF1/2 binding in mouse and human cell lines. |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We report ChIP-Seq analysis of the RNA polyemerase I trascription factor UBF1/2 in NIH3T3, HMEC and HMLER cell lines.
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| Overall design |
NIH3T3* samples:
We correlated UBF1/2 binding across the genome with that of RNA polemerase I (Pol I), RNA polemerase II (Pol II) and chromatin states in NIH3T3 cells
We perfromed ChIP-seq of UBF1/2 (2 biological replicates), Pol I (POLR1A/RPA194), Pol II, H3K9me3, H3K4Me3, H3K9ac, H4 hyperacetylation and genomic DNA input as reference.
HMEC* samples:
We report ChIP-Seq analysis of UBF1/2 and Pol I (POLR1A/RPA194) in human mammary epithelial cells (HMEC). In addition we include UBF1/2 ChIP-seq in the tumourigenic epithelial cell line HMLER. In this study, we compared UBF1/2 binding in HMEC to UBF1/2 binding in in the tumorigenic HMLER cells, an isogenic HMEC-derived cell line expressing the SV40 large-T, TERT, and an oncogenic allele of the HRAS gene (expressing HRASV12G) that forms tumors in nude mice (Elenbaas et al., Gene & Development 2001)
We sequenced UBF1/2 ChIP and Pol I(POLR1A/RPA194) ChIP and gDNA input from HMEC. We sequenced UBF1/2 ChIP and gDNA input from HMLER
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| Contributor(s) |
Sanij E, Hannan R |
| Citation(s) |
25452314 |
| BioProject |
PRJNA239280 |
| Submission date |
Nov 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Elaine Sanij |
| E-mail(s) |
elaine.sanij@petermac.org
|
| Phone |
+61396563758
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Department |
Research
|
| Lab |
Growth Control Laboratory
|
| Street address |
1 St Andrews Place
|
| City |
East Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3001 |
| Country |
Australia |
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| Platforms (3) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL15433 |
Illumina HiSeq 1000 (Homo sapiens) |
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| Samples (10)
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| Relations |
| SRA |
SRP039369 |
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