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

Human NTERA2 (NT2/D1) cells lines: shZRF1 vs. shRandom during Retinoic Acid (RA) administration

Project description:Transcriptional profiling of human NT2 cell lines comparing control cells (shRandom) with ZRF1 knockdown cells (shZRF1) both either untreated (0 h) or treated with Retinoic Acid (3 h) at 0.01 µM. The cell lines were established by retroviral infection allowing for the transcription of either a random shRNA (shRandom) or a shRNA specific for ZRF1 (shZRF1). The goal was to determine the effect of ZRF1 on transcriptional activation at the onset of differentiation.

2010-12-24 | GSE16858 | GEO

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

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

2020-07-23 | GSE134493 | GEO

shRNA-mediated Myc knockdown and shRNA-mediated knockdown of Myc-induced lncRNA KTN1-AS1 in ST486 Burkitt lymphoma cells

Project description:shRNA-mediated Myc knockdown and shRNA-mediated knockdown of Myc-induced lncRNA KTN1-AS1 in ST486 Burkitt lymphoma cells

| PRJNA490714 | ENA

Effect of knockdown LINC01089 on gene expression in SK-Hep-1 cells

Project description:To explore the effect of LINC01089 on gene expression and alternative splicing, we established stable LINC01089 knockdown cell lines in SK cells and perfromed RNA-seq.

2023-09-20 | GSE243537 | GEO

ATAC-seq for E14 cells knockdown with siRNA or shRNA

Project description:ATAC-seq was performed on cells E14 cells knockdown with siRNA or shRNA

2023-03-08 | GSE167177 | GEO

ATAC-seq for E14 cells knockdown with siRNA or shRNA

Project description:ATAC-seq for E14 cells knockdown with siRNA or shRNA

| PRJNA703640 | ENA