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Next Generation Sequencing upon siRNA-mediated knockdown of EIF5A in MCF-7 cells.

ABSTRACT: Next Generation Sequencing upon siRNA-mediated knockdown of EIF5A in MCF-7 cells.

PROVIDER: PRJNA413359 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing upon siRNA-mediated knockdown of EIF5A in MCF-7 cells.

Project description:The goal of this study is to examine the effect of EIF5A knockdown on the MCF-7 transcriptome.

2018-04-09 | GSE104604 | GEO

Next Generation Sequencing upon siRNA-mediated knockdown of DRAIC in MCF-7 cells.

Project description:Next Generation Sequencing upon siRNA-mediated knockdown of DRAIC in MCF-7 cells.

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Next Generation Sequencing upon siRNA-mediated knockdown of DRAIC in MCF-7 cells.

Project description:The goal of this study is to examine the effect of DRAIC knockdown on the MCF-7 transcriptome.

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Project description:Genome-wide survey of ribosome collision [eif5A siRNA]

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siRNA RNA-seq from MCF-7 (ENCSR005AHI)

Project description:RNA-seq on MCF-7 cells treated with siRNA targeting ZFX. 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

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Next generation sequencing of the transcriptome in MCF-7 cells with/without SRA knockdown

2014-01-23 | GSE52385 | GEO

Next generation sequencing of the transcriptome in MCF-7 cells with/without SRA knockdown

Project description:We employed next generation sequencing to examine whether knocking down the steroid receptor RNA activator (SRA) gene significantly affect the expression levels of certain genes in MCF-7 cells. MCF-7 cells were transfected with either a pool of four non-target control siRNAs or a pool of four SRA siRNAs for 32 hrs. 157 million reads were generated from triplicate samples of the control group; 151 million reads were generated from triplicate samples of the SRA knockdown group. Six genes were identified as significantly changed in the expression levels with the cutoff of q value ≤ 0.05, fold change ≤ 0.5 or ≥ 2, and reads per kilobase per million mapped reads (RPKM) ≥ 1. However, except for SRA itself, the other five genes were shown by real-time PCR to be only affected by one siRNA in the SRA siRNA pool. Further analysis of this dataset with different cuttoff setting may reveal true SRA-regulated genes in MCF-7. MCF-7 cells were cultured in high glucose DMEM with 10% fetal bovine serum, 2 mM Glutamax-1, 100 units/ml penicillin and 100 μg/ml streptomycin. ON-TARGETplus SMARTpool for human SRA (Thermo Scientific, L-027192-00-0005) was used to knockdown SRA (siSRA) and ON-TARGETplus Non-targeting Pool Thermo Scientific, D-001810-10-05) was used as a negative control (siCtrl). A total of 25 nM siRNA was transfected in 6-well dishes using Lipofectamine™ RNAiMAX Reagent (Life Technologies, Invitrogen) following the manufacturer’s recommendations. Polyadenylated RNA was purified from the cells 32 hrs after transfection. cDNA libraries were prepared and double-stranded cDNA was fragmented using DNase I according to Illumina specifications, prior to adaptor ligation. Sequencing libraries were amplified and sequenced using an Illumina HiSeq 2000 sequencer.

2014-01-23 | E-GEOD-52385 | biostudies-arrayexpress

Ribosome profiling study of eIF5A depletion strain

Project description:The eukaryotic translation factor eIF5A, originally identified as an initiation factor, was later shown to promote translation elongation of iterated proline sequences. Using a combination of ribosome profiling and in vitro biochemistry, we report a much broader role for eIF5A in elongation and uncover a substantial function for eIF5A in termination. Ribosome profiling of an eIF5A-depleted strain reveals a global elongation defect, with abundant ribosomes stalling at many sequences, not limited to proline stretches. Our data also show accumulation at stop codons and in the 3’-UTR, suggesting a global defect in termination in the absence of eIF5A. Using an in vitro reconstituted translation system, we find that eIF5A strongly promotes the translation of novel stalling sequences and increases the rate of peptidyl-tRNA hydrolysis more than 17-fold. We conclude that eIF5A functions broadly in elongation and termination, rationalizing its great cellular abundance and essential nature.

2017-04-07 | GSE89704 | GEO

Gene expression data from human breast cancer MCF-7 cells treated with siRNA targeting PSF or NONO

Project description:To examine the role of PSF and NONO in estrogen-dependent breast cancer, MCF-7 cells were treated with siRNA targeting PSF, NONO or control siRNA (siControl). Microarray analysis revealed PSF- or NONO-regulated genes in MCF-7 cells.

2020-01-13 | GSE132743 | GEO

Gene expression altered by HOTAIR knockdown in MCF-7-TNR

Project description:The human HOTAIR-specific siRNA and control siRNA were transfected into MCF-7-TNR cells. RNA was collected at 72 hrs after transfection. RNA-SEQ was carried out to profile the gene expression altered by HOTAIR knockdown.

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