Homo sapiens
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-42735
PROVIDER: PRJNA182963 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR628721.fastq.gz | Fastqsanger.gz | |||
| SRR628722.fastq.gz | Fastqsanger.gz | |||
| SRR628723.fastq.gz | Fastqsanger.gz | |||
| SRR628724.fastq.gz | Fastqsanger.gz | |||
| SRR628725.fastq.gz | Fastqsanger.gz |
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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
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.
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Project description:Genome-wide transcriptome profiling of SK-Mel-28, UACC-62 and HCT-116 cells stably expressing scrambled shRNA and RAB7 shRNA
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Project description:We have identified CUGBP1 dependent regulation of cell cycle and DNA replication/synthesis networks in melanoma cells. This data set we include gene expression and alternative splicing data of control and CUGBP1 depleted melanoma cell lines (SK-Mel-103 and UACC-62).
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Project description:Expression profiles of ADORA1-shRNA-transfected Sk-mel-28 human melanoma cell line and scrambled-shRNA control cells
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Project description:Oncolytic viral therapy represents an alternative therapeutic strategy for the treatment of cancer. This therapy relies on efficient replication of virus in tumor cells in vivo with minimal or no replication in normal tissues. We recently described GLV-1h68 as a modified Vaccinia Virus (VACV) construct with exclusive in vivo tropism for tumor cells in experimental animal models. Moreover, we had previously observed a cell line-specific relationship between the ability of GLV-1h68 to replicate in vitro during the first 20 hours following infection and the in vivo ability to colonize and eliminate the corresponding tumor implant. Thus, we surveyed the in vitro permissivity to GLV-1h68 replication of the NCI-60 panel of cell lines, extensively characterized and used for the assessment of novel therapeutic modalities. All cell lines were cultured and infected in identical conditions. Pre-infection transcriptional profiling was obtained to search for correlates of permissivity to viral infection. Selected cell lines were also tested for permissivity to another VACV and a vesicular stomatitis virus (VSV) strain. We observed that permissivity to VACV infection during the first 20 hours is quite heterogeneous among cell lines but highly reproducible within each cell line. The tissue of origin of each cell line does not influence permissivity to infection with the exception of B cell derivation. Permissivity correlates between two VACV constructs and between them and VSV suggesting a common permissive phenotype. No clear transcriptional pattern predictive of permissivity to infection could be identified though weak associations were observed that suggest a multifactorial control of viral replication. This study adds to the current characterization of the NCI-60 panel to guide the design and interpretation of experimental models testing oncolytic therapies. Seventy-four microarray samples were obtained from 8 renal cancer cell lines (786-0, A498, ACHN, CAKI-I, RXF-393, SN12C, TK-10, UO-31); 12 melanoma cell lines (888-MEL, 1858-MEL, 1936-MEL, 397, A375-MEL, LOX IMVI, M14, SK-MEL-2, SK-MEL-5, SK-MEL-28, UACC 62, UACC 257 ); 11 lung cancer cell lines (A549 p7, A549 p107, EKVX, HOP-62, HOP-92, NCI-H23, NCI-H226, NCI-H322M, NCI-H460, NCI-H522, NCI-H1299); 13 colon cancer cell lines (HCT-15, HCT-116, HT-29 p155, HT-29 p9, KM-12, SW-620, Colo 205, HCC 2998, NCI-ADR-RES, OVCAR 3 p7, OVCAR 3 p42, OVCAR 5, SK-OV-3); 3 ovarian cancer cell lines (OVCAR 4, OVCAR 8, IGROV); 1 cervical cancer cell line (Siha); 6 brain cancer cell lines (SNB 19, SF 295, SF 298, SNB 75, U251, SF 539); 7 breast cancer cell lines (BT-549, GI101A, HS-578T, MCF 7, MDA-MB-231 p41, MDA-MB-435, MDA-MB-231 p6); 7 hematopoietic cancer cell lines (CCFR-CEM, HL-60, K-562, MOLT-4, RPMI 8226, SR, T-47D); 3 prostatic cancer cell lines (Du-145, PC 3 p7, PC 3 p35); 1 hepatic cancer cell lines (Huh 7.5.1); and 2 pancreatic cancer cell lines (MIA PACA 2, Panc 1). Two technical repeats were performed (cell lines Siha and SNB-19). Reference T-RNA was obtained from 6 normal donor PBMCs.
2012-03-24 | E-GEOD-28472 | biostudies-arrayexpress
Project description:p62/SQSTM1 was identified as a modulator of metastatic genes selectively enriched in melanoma in autophagy independent manner. iTRAQ quantitative proteomic approach was performed in melanoma cell lines (SK-Mel-103 and UACC-62) deficient for p62 to identify downstream effectors of p62. Similar studies were performed for ATG5, a core component of autophagy, as a reference for autophagy-associated changes in protein abundance. Additionally, melanoma cells were subjected to affinity purification (AP-MS) to identify the interactors of p62. Overall, these studies underscore a novel unexpected role of p62 regulating the stability of prometastatic factors via the interaction with RNA Binding Proteins, thus leading to the inhibition of protein translation.
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Project description:p62/SQSTM1 was identified as a modulator of metastatic genes selectively enriched in melanoma in autophagy independent manner. iTRAQ quantitative proteomic approach was performed in melanoma cell lines (SK-Mel-103 and UACC-62) deficient for p62 to identify downstream effectors of p62. Similar studies were performed for ATG5, a core component of autophagy, as a reference for autophagy-associated changes in protein abundance. Additionally, melanoma cells were subjected to affinity purification (AP-MS) to identify the interactors of p62. Overall, these studies underscore a novel unexpected role of p62 regulating the stability of prometastatic factors via the interaction with RNA Binding Proteins, thus leading to the inhibition of protein translation.
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