Project description:shRNA knockdown against HNRNPA1 in HepG2 cells followed by RNA-seq. (HNRNPA1-BGHLV20) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:F-box only protein 38 (FBXO38), which belongs to SKP1-CUL1-F-box protein (SCF) family, exhibits the ability to mediate Lys48-linked poly-ubiquitination and subsequent proteasome degradations of PD-1.To investigate the effect of FBXO38 knockdown on transcription in tumor, we constructed control and FBXO38 knockdown by shRNA in Hela and HCT116 cell lines. We found that FBXO38 may interact with the immune pathway in the tumor.
Project description:Dicer and Argonaute2 (Ago2) gene is involving in microRNA (miRNA) maturation. Knockdown of these genes has great impact on miRNA expression profiles. We used microarrays to detail the miRNA expression profiles in Dicer- and Ago2-knockdown HeLa cells and demonstarted that the significant difference between Ago2-knockdown and Dicer- and Ago2-co-knockdown HeLa cells were not found.
Project description:RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA1. (HNRNPA1_BGKLV21-B) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:Mediator complex has been known as pivotal regulator of RNA polymerase II. Mediator complex has two CDK subunits in vertebrates, named CDK8 and CDK19. To elucidate functional difference between CDK8 and CDK19 in human cell, we employ siRNA mediate knockdown assay using HeLa S3 cell line. According to this assay these CDKs possess highly redundancy in HeLa S3 cell transcription regulation mechanism but in several genes, each CDK shows gene specific regulatory function. HeLa S3 cells were seeded on 6-well plate at 4 x 104 cells per well in 2ml antibiotic free DMEM medium before 24hr transfection. We transfect siRNA using Lipofectamine 2000 (invitrogen) according to its manual and siRNA final concentration in the medium was 20nM. After culturing for 48hr, transfection medium was changed to fresh antibiotic containing medium. Then the cells were incubated for additional 12hr and then RNA was prepared using RNeazy column (QIAGEN). Five μg of prepared RNA was subjected to the gene expression analysis using Human Genome U133 Plus 2.0 (Affymetrix) followed by characterizations with GeneSpring software (Agilent) and Pathway Analysis software (Ingenuity). In this analysis we employ two individual siRNA against each CDK and three replicates in each condition.
Project description:Mediator complex has been known as pivotal regulator of RNA polymerase II. Mediator complex has two CDK subunits in vertebrates, named CDK8 and CDK19. To elucidate functional difference between CDK8 and CDK19 in human cell, we employ siRNA mediate knockdown assay using HeLa S3 cell line. According to this assay these CDKs possess highly redundancy in HeLa S3 cell transcription regulation mechanism but in several genes, each CDK shows gene specific regulatory function. HeLa S3 cells were seeded on 6-well plate at 4 x 104 cells per well in 2ml antibiotic free DMEM medium before 24hr transfection. We transfect siRNA using Lipofectamine 2000 (invitrogen) according to its manual and siRNA final concentration in the medium was 20nM. After culturing for 48hr, transfection medium was changed to fresh antibiotic containing medium. Then the cells were incubated for additional 12hr and then RNA was prepared using RNeazy column (QIAGEN). Five μg of prepared RNA was subjected to the gene expression analysis using Human Genome U133 Plus 2.0 (Affymetrix) followed by characterizations with GeneSpring software (Agilent) and Pathway Analysis software (Ingenuity). In this analysis we employ two individual siRNA against each CDK and three replicates in each condition.
