Total RNA was isolated from 22Rv1 cells treated with 10 μM VNPP433-3β for 24 h in triplicates using RNAeasy Plus mini kit (Qiagen, Hilden, Germany). The RNA was quantified, and the quality of preparation was assessed using Agilent 2100 Bioanalyzer. Only preparations with RNA Integrity Number (RIN) 8 or above was considered for the preparation of library using NEB Ultra II Directional RNA library prep kit. The libraries were quality-checked using Qubit and Agilent 2100 Bioanalyzer. RNA sequencing was carried out in Illumina NovaSeq S2 PE100 bp lane at Maryland Genomics, Institute for Genome Sciences, University of Maryland Baltimore. The quality of sequencing was measured by Phred quality score (Q score). Differential gene expression and Gene Set Enrichment analyses (GSEA) were carried out to reveal the genes and cellular metabolic and signaling pathways modulated by VNPP433-3β.
Novaseq s2 pe100 bp lane
Manufactured by Illumina
The NovaSeq S2 PE100 bp lane is a high-throughput sequencing platform from Illumina. It is designed to generate 100 base pair paired-end reads. The core function of this product is to perform DNA sequencing for a variety of applications.
Automatically generated - may contain errors
Lab products found in correlation
Agilent 2100 bioanalyzer, by Agilent Technologies (4 mentions)
Rnaeasy plus mini kit, by Qiagen (3 mentions)
Neb ultra 2 directional rna library prep kit, by New England Biolabs (1 mentions)
Rneasy plus mini kit, by Qiagen (1 mentions)
Ultra 2 directional rna library prep kit, by New England Biolabs (1 mentions)
4 protocols using novaseq s2 pe100 bp lane
1
Transcriptomic Analysis of VNPP433-3β in 22Rv1 Cells
2
VNPP433-3β Transcriptome Analysis in CWR22Rv1 Cells
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Total RNA was isolated from CWR22Rv1 cells treated with 10 μM VNPP433‐3β (24 h) using RNeasy Plus mini kit (Qiagen) following manufacturer's instructions. DMSO vehicle control and drug treatment were performed in triplicates and all RNA samples were quantified and quality‐checked using Agilent 2100 Bioanalyzer. Only RNA preps having an RNA Integrity Number (RIN) of 8 or above were considered for RNA‐seq experiments. NEB Ultra II Directional RNA library prep kit was used for preparing RNA‐Seq libraries. The libraries thus generated were evaluated for size distribution and yield using Qubit and Agilent 2100 Bioanalyzer. RNA sequencing was conducted on Illumina NovaSeq S2 PE100 bp lane at Maryland Genomics, Institute for Genome Sciences, University of Maryland, Baltimore. The quality of sequencing was measured by Phred quality score (Q score) and more than 90% of the sequencing reads attained Q30 (99.9% base call accuracy). GO and GSEA were carried out using GSEA v4.2.2 against Molecular Signatures Database v7.5.1 with permutation set at “gene set” and other parameters default.15 Qiagen IPA was carried out to uncover canonical pathways modulated by VNPP433‐3β.
3
Transcriptional Profiling of VNLG-152R-Treated MDA-MB-231 Cells
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MDA-MB-231 cells were treated with 10 μM VNLG-152R for 24 h in triplicates. Total RNA was isolated using RNAeasy Plus mini kit (Qiagen) following manufacturer’s instructions. The RNA preparation was quantified and assessed its quality using Agilent 2100 Bioanalyzer. A RIN value of 8 or above was used for all samples. The sequencing libraries were prepared with the NEB Ultra II Directional RNA library prep kit. Further, the libraries were evaluated for quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer. Sequencing was carried out on an Illumina NovaSeq S2 PE100 bp lane (Maryland Genomics, Institute for Genome Sciences, University of Maryland Baltimore). As a norm, Phred quality score (Q score; to measure the quality of sequencing) more than 90% of the sequencing reads reached Q30 (99.9% base call accuracy). Differential Gene Expression and Gene Set Enrichment analyses (GSEA) were performed to identify canonical cellular pathways modulated by VNLG-152R as reported previously (28 (link)).
4
Transcriptomic Analysis of VNPP433-3β in CWR22Rv1 Cells
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CWR22Rv1 cells were treated with 10 μM VNPP433-3β for 24 or 48 h in triplicates. Cells were then washed with PBS and RNA was extracted using RNAeasy Plus mini kit (Qiagen, Hilden, Germany). The concentration and quality of total RNA samples were assessed using Agilent 2100 Bioanalyzer, and a RIN (RNA Integrity Number) threshold of 8 or above was employed for all samples. RNA-Seq libraries were prepared with the NEB Ultra II Directional RNA library prep kit. The libraries were assessed for quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer. Sequencing was performed on an Illumina NovaSeq S2 PE100 bp lane at Maryland Genomics, Institute for Genome Sciences, University of Maryland Baltimore. Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy). QIAGEN Ingenuity Pathway and Gene Set Enrichment analyses (GSEA) were carried out to reveal canonical cellular pathways modulated by VNPP433-3β.
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