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Analysis of FGF20-regulated genes in differentiating cochlear hair and supporting cell progenitors via ribosome affinity purification

ABSTRACT: Analysis of FGF20-regulated genes in differentiating cochlear hair and supporting cell progenitors via ribosome affinity purification

PROVIDER: PRJNA624110 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11518846.fastq.gz	Fastqsanger.gz
	SRR11518847.fastq.gz	Fastqsanger.gz
	SRR11518848.fastq.gz	Fastqsanger.gz
	SRR11518849.fastq.gz	Fastqsanger.gz
	SRR11518850.fastq.gz	Fastqsanger.gz

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Analysis of FGF20-regulated genes in differentiating cochlear hair and supporting cell progenitors via ribosome affinity purification

Project description:Background: Understanding the developmental mechanisms that regulate hair cell differentiation in the cochlea is essential to designing genetic therapies for acquired hearing loss due to hair cell loss or damage. We have previously identified Fibroblast Growth Factor 20 (FGF20) as having a key role in hair cell and supporting cell differentiation and patterning in the mouse cochlear sensory epithelium. To investigate the genetic landscape regulated by FGF20 signaling in hair cell and supporting cell progenitors, we employ Translating Ribosome Affinity Purification (TRAP) combined with Next Generation mRNA Sequencing (TRAPseq). Methods: In mice, we used Fgf20-Cre to activate ROSA-fsTRAP in hair cell and supporting cell progenitors, and then collected translating mRNA using TRAP from Fgf20+/- (control) and Fgf20-/- cochleae. Library preparation and sequencing were done in two separate experiments, each with 12 samples that included 2 pre-TRAP (pre-immunoprecipitation) Fgf20+/- samples, 2 TRAP Fgf20+/- samples, 4 pre-TRAP Fgf20-/- samples, and 4 TRAP Fgf20-/- samples. Samples were sequenced via Illumina HiSeq 3000. We compared pre-TRAP (pre-immunoprecipitation) samples with TRAP mRNA samples to validate the TRAP technique as well as identify genes enriched in our target cell population. We also compared Fgf20+/- and Fgf20-/- TRAP mRNA samples to identify differentially expressed genes downstream of FGF20 during hair cell and supporting cell differentiation. Results: TRAPseq targeting the prosensory cell population effectively enriches for translating mRNA within this rare cell population. TRAPseq comparing Fgf20+/- and Fgf20-/- samples identified differentially expressed genes downstream of FGF20. These included FGF-response genes Etv4, Etv5, Etv1, and Dusp6, as well as genes associated with cochlea development and hearing, such as Hey1, Hey2, Heyl, Tectb, Fat3, Cpxm2, Sall1, and cell cycle regulators such as Cdc20.

2020-04-10 | GSE148380 | GEO

RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]

Project description:This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 1 and postnatal day 6. mRNA profiles of supporting cells (GFP+) and all other cochlear cell types (GFP-), two replicates each, at P1 and P6 mice were generated by deep sequencing using Illumna TruSeq.

2016-07-01 | E-GEOD-83356 | biostudies-arrayexpress

RNA-seq analysis of neonatal mouse cochlear supporting cells [Treated AK]

Project description:This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6 after inhibition of the Notch signaling pathway. Cochleas from postnatal day 0 and postnatal day 5 were cultured for 24 hours in the gamma secretase inhibitor DAPT or DMSO as a vehicle control. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 0+24 hours culture and postnatal day 5 + 24 hours culture. (corresponding to P1 and P6). mRNA profiles of P0 and P5 supporting cells (GFP+) and all other cochlear cell types (GFP-) treated with DAPT or DMSO, two replicates each, were generated by deep sequencing using Illumna TruSeq.

2016-07-01 | E-GEOD-83340 | biostudies-arrayexpress

RNA-seq analysis of neonatal mouse cochlear supporting cells [NonTreated_JM]

2016-07-01 | GSE83356 | GEO

RNA-seq analysis of neonatal mouse cochlear supporting cells [Treated AK]

2016-07-01 | GSE83340 | GEO

RNA-seq analysis of neonatal mouse cochlear supporting cells

Project description:RNA-seq analysis of neonatal mouse cochlear supporting cells

| PRJNA325664 | ENA

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus RsaG sRNA targetome

Project description:MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus RsaG sRNA targetome. Affinity purification of in vivo regulatory complexes coupled with high throughput RNA sequencing methodology or MAPS standing for “MS2 affinity purification coupled to RNA".

2024-06-01 | GSE176028 | GEO

Intrinsic regenerative potential of murine cochlear supporting cells

Project description:P3 Math1-nGFP mouse cochlear sensory epithelia, consisting of greater and lesser epithelial ridges (GER & LER) including the organ of Corti with nGFP-positive hair cells, were dissected, dissociated into single cells, and labeled with propidium iodide and three CD marker antibodies. The cell suspension was subjected to FACS purification. 83.6 ±2.8% of the total input of cells were viable, determined by exclusion of propidium iodide. Only viable cells were collected into 5 distinct populations: GFP+ cells (Samples HC_A-D), GFP?/CD271High (Samples Mac_A-C), as well as GFP?/CD271Low/CD326+/CD146Low (Samples SC_A-B), GFP?/CD271Low/CD326+/CD146Hig (Samples GER_A-B), and GFP?/CD271Low/CD326? (Sample BM_B). Please see Sinkkonen et al 2011 PMID: 22355545 Total RNA was isolated from 5 different FACS sorted cell poulations from P3 Math1-nGFP cochlea.

2014-10-22 | E-GEOD-62582 | biostudies-arrayexpress

DNA affinity purification sequencing (DAP-seq) data of LEAFY (LFY)

Project description:In this study, we use DNA affinity purification sequencing to identiy genome-wide binding of LFY transcription factor, a master regulator of flower development in Arabidopsis. We generated two sets of data, one using genomic DNA from plant tissue, thus retain DNA methylation, as probe for DNA affinity purification (DAP-seq dataset), and the other using PCR amplified genomic DNA (without DNA methylation; AmpDAP-seq dataset).

2021-03-25 | GSE160013 | GEO

Reprogramming of cochlear supporting cells by MYC/NICD co-activation.

Project description:Reprogramming of cochlear supporting cells by MYC/NICD co-activation.

| PRJNA844057 | ENA