Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of ADORA1 knockdown and scrambled-shRNA control cells' Transcriptomes

ABSTRACT: Expression profiles of ADORA1-shRNA-transfected Sk-mel-28 human melanoma cell line and scrambled-shRNA control cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE134493 | GEO | 2020/07/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide transcriptome profiling of SK-Mel-28, UACC-62 and HCT-116 cells stably expressing scrambled shRNA and RAB7 shRNA

Project description:Purpose: Assess the transcriptional changes induced upon RAB7 knock-down in melanoma (SK-Mel-28 and UACC-62) and in colon cancer (HCT-116) cell lines. Methods: mRNA profiles of tumor cell lines (SK-Mel-28, UACC-62, HCT-116) stably expressing scrambled shRNA or RAB7 shRNA (harvested at day 3 after lentiviral infection) were generated by deep sequencing, using three biological replicates per condition. The sequence reads that passed quality filters were analyzed with TopHat and Cufflinks. Validation of induced / silenced genes was performed by western blot. Results show a differential impact of RAB7 expression in the transcriptomic profile of melanoma vs non-melanoma cell lines, and support a lineage-specific role of this small GTPase in melanoma. Examination of the mRNA profiles RAB7-depleted vs wild type cells, performed in parallel in 3 different tumor cell lines (Melanomas: SK-Mel-28 and UACC-62, Non-melanoma: HCT-116) harvested at day 3 after lentiviral infection.

2014-04-20 | E-GEOD-42735 | biostudies-arrayexpress

Genome-wide transcriptome profiling of SK-Mel-28, UACC-62 and HCT-116 cells stably expressing scrambled shRNA and RAB7 shRNA

Project description:Purpose: Asess the transcritpional changes induced upon RAB7 knock-down in melanoma (SK-Mel-28 and UACC-62) and in colon cancer (HCT-116) cell lines. Methods: mRNA profiles of tumor cell lines (SK-Mel-28, UACC-62, HCT-116) stably expressing scrambled shRNA or RAB7 shRNA (harvested at day 3 after lentiviral infection) were generated by deep sequencing, using three biological replicates per condition. The sequence reads that passed quality filters were analyzed with TopHat and Cufflinks. Validation of induced / silenced genes was performed by western blot. Results show a differential impact of RAB7 expression in the transcriptomic profile of melanoma vs non-melanoma cell lines, and support a lineage-specific role of this small GTPase in melanoma.

2014-04-20 | GSE42735 | GEO

PHF19 shRNA or scrambled control shRNA

Project description:PHF19 shRNA or scrambled control shRNA

| PRJNA1070967 | ENA

Lentiviral shRNA library screen to identify growth-related genes in malignant melanoma

Project description:Little is known about genes that promote melanoma cell growth and proliferation. siRNAs may be used to address the role of individual genesin these processes. RNAi library screens were used in the past to gain a comprehensive overview of all genes involved in cell growth, proliferation, migration and other cellular processes. A large-scale loss-of-function screen for eight different melanoma cell lines was performed using a pooled lentiviral shRNA library (GeneNet Human 50K lentiviral shRNA Library,cat#SI206B-1, System Biosciences) to identify genes relevant for melanoma cell growth and proliferation. shRNAs that lead to cell death or reduced growth of transduced melanoma cells are negatively selected and thereby underrepresented in the final cellular shRNA pool and vice versa. The shRNAs of the shRNA library (3-5 per gene) have complementary sequences to probes on the custom Affymetrix microarray HG-U133Plus2 and were analysed using this array. Well-known melanoma cell lines SK-Mel-103, A375, SK-Mel-147, SK-Mel-19, SK-Mel-28, SK-Mel-29, SK-Mel-5, WM3523cln6 were transduced with the lentiviral shRNA library and grown for 10 days under puromycin selection (day 10), control cells of respective cell lines were transduced and frozen immediately after transduction and genomic integration of shRNAs (day 0). Totel DNA was extracted and genomically integrated shRNAs were hybridized to Affymetrix microarrays (HG-U133Plus2.0 array).

2014-01-24 | E-GEOD-46675 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of ADORA1 knockdown and scrambled-shRNA control cells' Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of ADORA1 knockdown and scrambled-shRNA control cells' Transcriptomes

| PRJNA555332 | ENA

The global transcriptome analysis of HCT116 cells transfected with scrambled or CBX4 shRNA

Project description:To investigate the molecular mechanism of CBX4 in CRC, the global transcriptomes were analyzed in HCT116 cells in which CBX4 was knocked down with shRNA, and these transcriptomes were compared to those of HCT116 cells transfected with scrambled shRNA.

2017-02-10 | GSE87778 | GEO

RNA sequencing in the Kasumi-1 cell line transfected with PHF19 shRNA or scrambled control shRNA

Project description:RNA sequencing in the Kasumi-1 cell line transfected with PHF19 shRNA or scrambled control shRNA

| PRJNA1070965 | ENA

shRNA profiling of human myeloma cell line jjn3 with non-specific, scrambled shrna or cks1b shrna

Project description:This series represents Affymetrix U133Plus2.0 data sets of JJN3 transduced with levivirus expressing non-specific scrambled shRNA or CKS1B shRNA Experiment Overall Design: This series represents Affymetrix U133Plus2.0 data sets of JJN3 transduced with levivirus expressing non-specific scrambled shRNA or CKS1B shRNA

2008-06-12 | E-GEOD-3369 | biostudies-arrayexpress

Affymetrix U133Plus2.0 data sets of Human Myeloma Cellline JJN3 with non-specific, scrambled shRNA or CKS1B shRNA

Project description:This series represents Affymetrix U133Plus2.0 data sets of JJN3 transduced with levivirus expressing non-specific scrambled shRNA or CKS1B shRNA Keywords: JJN3 CKS1B shRNA

2006-03-31 | GSE3369 | GEO

Homo sapiens

Project description:Genome-wide transcriptome profiling of SK-Mel-28, UACC-62 and HCT-116 cells stably expressing scrambled shRNA and RAB7 shRNA

| PRJNA182963 | ENA