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Bulk sequencing of MYCN-overexpressing chicken retinal cell lines

ABSTRACT: Bulk sequencing of MYCN-overexpressing chicken retinal cell lines

PROVIDER: PRJNA818671 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18432465_1.fastq.gz	Fastqsanger.gz
	SRR18432465_2.fastq.gz	Fastqsanger.gz
	SRR18432466_1.fastq.gz	Fastqsanger.gz
	SRR18432466_2.fastq.gz	Fastqsanger.gz
	SRR18432467_1.fastq.gz	Fastqsanger.gz

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Bulk RNA-sequencing of MYCN-overexpressing chicken retinal cell lines

Project description:Bulk RNA-sequencing of MYCN-overexpressing chicken retinal cell lines

| PRJNA940372 | ENA

Bulk sequencing of MYCN-overexpressing chicken retinal cell lines

Project description:Background: MYCN gene is a transcription factor whose amplification and overexpression can lead to tumorigenesis. In retina, MYCN overexpression is related to tumorigenesis of retinoblastoma, a childhood cancer. Purpose: To find out differentially expressed genes in MYCN-overexpressing cells, which will give information of MYCN-related gene expression and possibly find out new pathways in mechanism of retinoblastoma tumorigenesis with MYCN overexpression. Methods: MYCN-overexpressing cells were taken from MYCN electroporated E14 chicken retina and kept in culture for over 4 weeks. Unelectroporated E14 chicken retina central region was dissected as a control. Total RNA was extracted and sequenced on Illumina NovaSeq 6000. The data were used for differential expression analysis and GO/Pathway enrichment analysis. Results: Genes related to proliferation were upregulated in MYCN-overexpressing cells, while genes related to neural differentiation were downregulated. GO/Pathway enrichment analysis showed that upregulated genes were enriched for pathways associated with cell proliferation and downregulated genes for neural differentiation.

2022-06-30 | GSE199162 | GEO

Bulk RNA-sequencing of MYCN-overexpressing chicken retinal cell lines

Project description:Background: MYCN gene is a transcription factor whose amplification and overexpression can lead to tumorigenesis. In retina, MYCN overexpression is related to tumorigenesis of retinoblastoma, a childhood cancer. Purpose: To find out differentially expressed genes in MYCN-overexpressing cells, which will give information of MYCN-related gene expression and possibly find out new pathways in mechanism of retinoblastoma tumorigenesis with MYCN overexpression. Methods: MYCN-overexpressing cells were taken from MYCN electroporated E14 chicken retina and kept in culture. Unelectroporated E14 chicken retina central region was dissected as a control. Total RNA was extracted and sequenced on Illumina NovaSeq 6000. The data were used for differential expression analysis and GO/Pathway enrichment analysis.

2024-03-11 | GSE226458 | GEO

RNA-seq of human hTERT-RPE1 and RPE1-MYCN-ER cells with treatment of EtOH (0h) or tamoxifen for 24h, 48h and 72h to activate MYCN

Project description:RNA-seq upon MYCN activation in the hTERT-immortalized MYCN retinal pigmented epithelial cell line (RPE1–MYCN-ER). The parental hTERT-immortalized retinal pigment epithelium (hTERT-RPE1) was used as a control as this cell line does not carry the MYCN:ER expression construct. Both cell lines were treated with tamoxifen (400nM; 4-OHT) for MYCN induction (with 4-OHT or not). Analysis was performed 24 h, 48 h and 72 h upon MYCN activation, including four biological replicates per condition.

2021-06-03 | E-MTAB-9667 | biostudies-arrayexpress

Bulk RNA-seq analysis of Type 5 retinal bipolar cells from the Htr3a-GFP line

Project description:15,000 GFP+ cells were collected from two replicates of the Htr3a GFP line into RNAlater (ThermoFisher, AM7024). RNA was purified and bulk RNA-seq was performed using the Ovation RNA-seq system V2 (Nugen, 7102-32) Bulk RNA-seq analysis of Type 5 retinal bipolar cells (2 biological replicates)

2016-08-25 | E-GEOD-81902 | biostudies-arrayexpress

Single cell RNA-seq of human RPE1-MYCN-ER cells with treatment of EtOH (0h) or tamoxifen for 22h, 23h and 24h to activate MYCN.

Project description:Single cell RNA-seq upon MYCN activation in the hTERT-immortalized MYCN retinal pigmented epithelial cell line (RPE1–MYCN-ER). The cell line was treated with tamoxifen (400nM; 4-OHT) for MYCN induction (with 4-OHT or not). Analysis was performed 22h, 23h, and 24 h upon MYCN activation.

2021-12-01 | E-MTAB-9689 | biostudies-arrayexpress

Retinal-cysteine adduct in Opn5L1

Project description:Targeted analysis of retinal-cysteine adduct in Opsin 5 like-1 (Opn5L1) protein Chicken Opn5L1 E177K/Q192K mutant was expressed in HEK293T, regenerated by all-trans-retinal, solubilized by dodecyl maltoside, and purified using Rho1D4 antibody-conjugated Sephalose. Semi-quantitative targeted analyses of trypsinized Opn5L1 with or without light irradiation were carried out using reverse phase LC-ESI-MSn to detect light-dependent formation of retinal-cysteine adduct. The results were analyzed by Mass++, mMass and Igor Pro softwares.

2018-02-15 | PXD008890 | JPOST Repository

Transcriptional profiles of transgenic ALK^F1174L/MYCN vs. MYCN tumors

Project description:The ALK^F1174L mutation is associated with intrinsic and acquired resistance to crizotinib and cosegregates with MYCN in neuroblastoma. In this study, we generated a mouse model overexpressing ALK^F1174L in the neural crest. Comapred to mice expressing ALK^F1174L or MYCN alone, combined expression of the two aberrations led to development of neuroblastoma with a shorter latency and higher penetrance. Here, we evaluated the transcriptional profiles of MYCN-driven neuroblastomas with or without the expression of ALK^F1174L to determine the pathogenic consequences of the ALK^F1174L/MYCN interaction in neuroblastoma. 10 mice were analysed in this study. Five ALK^F1174L/MYCN tumors were compared with five MYCN tumors. Total RNA was extracted, samples were labeled and processed using the Agilent Low Input Quick Amp two color Cy3(sample) and Cy5 (mouse reference) labeling kit and hybridized to Agilent SurePrint G3 Mouse Gene Expression arrays.

2012-07-04 | E-GEOD-35560 | biostudies-arrayexpress

Transcriptional profiles of transgenic ALK^F1174L/MYCN vs. MYCN tumors

2012-07-05 | GSE35560 | GEO

Next generation sequencing of chicken otocyst with gain- and loss-of-Notch signalling activity

Project description:Bulk RNA-sequencing of individual chicken otocysts, in which Notch activity was either stimulated or blocked. To stimulate Notch activity, the E2 otic placodes were in ovo transfected with a construct overexpressing Notch1 Intracellular domain (NICD1) or a control plasmid expressing mRFP1 and collected 6h or 24h later. To pharmacologically block Notch activity, E2.5 chicken otocysts were incubated in media enriched with γ-secretase Inhibitor or control condition (DMSO) for 6h or 24h. Transcripts abundance was mapped to a chicken reference genome using Kallisto package.

2022-12-01 | GSE196999 | GEO

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