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RNA sequence analysis to compare alteration in transcriptome upon Elf5 loss in C3-T+ tumors

ABSTRACT: RNA sequence analysis to compare alteration in transcriptome upon Elf5 loss in C3-T+ tumors

PROVIDER: PRJNA503489 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8146220.fastq.gz	Fastqsanger.gz
	SRR8146221.fastq.gz	Fastqsanger.gz
	SRR8146212.fastq.gz	Fastqsanger.gz
	SRR8146222.fastq.gz	Fastqsanger.gz
	SRR8146213.fastq.gz	Fastqsanger.gz

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RNA sequence analysis to compare alteration in transcriptome upon Elf5 loss in C3-T+ tumors

Project description:The data generated here shows increased interferon gamma gene signatures in C3-T+ tumors with loss of Elf5

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RNA sequence analysis to compare Elf5+ and Elf5- tumor cells in C3-T; Elf5-GFP reporter mice tumors

Project description:The data generated here shows increased interferon gamma gene signatures in Elf5- tumor cells in C3-T; Elf5-GFP reporter mice tumors

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Project description:RNA sequence analysis to compare Elf5+ and Elf5- tumor cells in C3-T Elf5-GFP reporter mice tumors

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Transcript Profiling of Elf5+/- Mammary Glands During Pregnancy Identifies Novel Targets of Elf5

2010-09-27 | GSE23373 | GEO

MDA-MB-231 cell: infected with lentivirus to stably express mut-Elf5 vs WT-Elf5

Project description:Elf5 induced transcriptional changes in MDA-MB-231 origin, control (mut Elf5) vs WT ELF5

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MDA-MB-231 cell: infected with lentivirus to stably express mut-Elf5 vs WT-Elf5

Project description:Elf5 induced transcriptional changes in MDA-MB-231 origin, control (mut Elf5) vs WT ELF5 Two-condition experiment, control (mut-Elf5) vs WT-Elf5. Each has 3 biological repeats.

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Transcript Profiling of Elf5+/- Mammary Glands During Pregnancy Identifies Novel Targets of Elf5

Project description:Elf5, an epithelial-specific Ets transcription factor, plays a crucial role in the pregnancy-associated development of the mammary gland. However, the molecular mechanisms employed by Elf5 to exert its effects on the mammary gland are largely unknown. Transcript profiling was used to investigate the transcriptional changes that occur as a result of Elf5 haploinsufficiency. We show that the development of the Elf5+/- gland is delayed at a transcriptional and morphological level, due to the delayed increase in Elf5 protein in these glands. We also identify a number of potential Elf5 target genes, including Mucin 4, whose expression, is directly regulated by the binding of Elf5 to an Ets-binding site within its promoter. We identify novel transcriptional targets of Elf5 and show that Muc4 is a direct target of Elf5, further elucidating the mechanisms through which Elf5 regulates proliferation and differentiation in the mammary gland. We used Compugen 22,000 oligo arrays from the Adelaide Microarray Centre to determine the transcriptional effects of the loss of one Elf5 allele on mammary gland development. We examined Elf5+/+ and Elf5+/- mammary glands over 5 timepoints of mammary gland development in three experiments. Each experiment used the pooled RNA of 2 mice, resulting in a total of 6 individual mice at each timepoint per genotype. Replica 1 of each condition was labelled with the one fluorophore, and replicas 2 and 3 with the other fluorophore. A common reference design was used for this experiment. RNA extracted from eight pooled 17.5dpc C57BL/6 mouse embryos was used as the reference sample. In total, we performed 30 micraoarray hybridisations, examining 5 timepoints of mammary gland development in 2 genotypes (Elf5+/+ and Elf5+/-). This experiment was repeated with a total of three biological replicates.

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Gene expression in the development of C3 and C4 Atriplex and C3 Atriplex prostrata x C4 Atriplex rosea F1 hybrids

Project description:Elucidating the genetic control of development of C3 and C4 photosynthesis. Atriplex rosea (C4) and Atriplex prostrata (C3) were studied along a leaf developmental gradient to compare development between C3 and C4. C3 Atriplex prostrata x C4 Atriplex rosea F1 hybrid were studied along the same developmental gradient and will aid in identifying regulatory elements involved in C3 and C4 leaf development.

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Coordinate regulation of ELF5 and EHF at the chr11p13 modifier region

Project description:E74-like factor 5 (ELF5) and ETS-homologous factor (EHF) are epithelial selective ETS family transcription factors (TFs) encoded by genes at chr11p13, a region associated with cystic fibrosis (CF) lung disease severity. EHF controls many key processes in lung epithelial function so its regulatory mechanisms are important. Using CRISPR/Cas9 technology, we removed three cis-regulatory elements (CREs) from the chr11p13 region in airway epithelial cells. Deletion of two enhancers and one CRE within a stretch enhancer at the EHF locus caused subtle changes in chromatin architecture, and though EHF expression did not change, ELF5 abundance increased. ELF5 is normally very low in airway cells so we next examined cell types that express more ELF5 (LNCaP and T47D). ATAC-seq experiments in these lines revealed novel peaks of open chromatin (potential CREs) at the 5’ end of chr11p13 that were associated with an expressed ELF5 gene. Furthermore, 4C-seq assays identified direct interactions between the active ELF5 promoter and sites within the EHF locus, suggesting coordinate regulation between these TFs. ChIP-seq for ELF5 in T47D cells revealed ELF5 occupancy within EHF introns 1 and 6 and siRNA-mediated depletion of ELF5 repressed EHF expression. These results define a new role for ELF5 in lung epithelial biology.

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LM2 cell: infected with lentivirus to stably express Elf5 vs GFP

Project description:Elf5 induced transcriptional changes in high lung metastasis subline LM2 (MDA-MB-231 origin), control (GFP) vs ELF5

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