Human Epigenetic Factors Biology-on-Array

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Biology-on-Array

Human Epigenetic Factors siRNA System: TSPH-006A The Biology-on-Array is an innovative screening tool for identifying the transcription factors that regulate a gene of interest. This system utilizes real-time PCR as an end-point assay coupled with siRNA technology. The Human Epigenetic Factors siRNA plate includes siRNA pairs (2 pre-designed siRNAs per gene) for 84 key genes encoding enzymes and factors known to modify genomic DNA and histones to regulate chromatin accessibility and therefore gene expression. The de novo and maintenance DNA methyltransferases, and the enzymes responsible for demethylation of CpG dinucleotides are represented by the array. Enzymes catalyzing histone acetylation, methylation, phosphorylation, and ubiquitination are also included in the plate. The plate also analyzes involvement of genes encoding the SET domain proteins and SWI/SNF Complex Components, Polycombs and other chromatin remodeling factors. The knockdown of each specific transcription modulator results in a unique changes to the transcriptome. The high-throughput first strand kit enables conversion of 96 total RNA samples into cDNA. The real-time PCR assay can be used to analyze expression of any gene in these cDNA samples. The change in the expression of the gene in specific samples(s) reveals that corresponding epigenetic factor(s) are involved in controlling the expression of this gene.

Functional Gene Grouping

Kit Components

How It Works

Manuals & Data Analysis

Gene Table

Chromatin Modification Enzymes:

DNA Methyltransferases: DMAP1, DNMT1, DNMT3A, DNMT3B.
DNA / Histone Demethylases: AOF2, JARID1C.
Histone Methyltransferases: CARM1, EHMT2, MLL, MLL2, PRMT1, PRMT5, SMYD3, SUV39H1.
SET Domain Proteins (Histone Methyltransfesase Activity): SETD1A, SETD2, SETD7, SETD8, SETDB1, SUV39H1.
Histone Acetyltransferase: ATF2, CIITA, HAT1, KAT2B, MYST1, MYST2, NCOA1.
Histone Deacetylases: HDAC1, HDAC2, HDAC3, HDAC4, HDAC5, HDAC7, HDAC9.
Histone Phosphorylation: AURKA, AURKB, RPS6KA3.
Histone Ubiquitination: UBE2B.

Chromatin Remodeling Factors:

SWI/SNF Complex Components: ARID1A, ARID1B, INO80, PBRM1, RSF1, SMARCA1, SMARCA2, SMARCA4, SMARCA5, SMARCAL1, SMARCB1, SMARCC1, SMARCC2, SMARCD1, SMARCD3, SMARCE1, SRCAP.
Polycomb Group Genes: BMI1, EED, EZH2, SUZ12.
Bromodomain Proteins: BAZ1A, BAZ1B, BAZ2A, BRD2, BRD7.
Chromobox / Heterochromatin Protein 1 (HP1) Homologs: CBX1, CBX3, CBX5.
Chromodomain / Helicase / DNA-Binding Domain (CHD) Proteins: CHD1, CHD2, CHD3, CHD4, CHD5, CHD7.
Methyl-CpG DNA Binding Domain (MDB) Proteins: MBD1, MBD2, MBD3, MBD4, MECP2.
Nucleosome-Remodeling and Histone Deacetylase (NuRD) Complex Components: CHD3, MBD3, MTA1, MTA2, SPEN.
Inhibitor of Growth (ING) Family Members: ING1, ING2, ING4.

Transcription Factor: E2F6.

Functional Gene Grouping

Kit Components

How It Works

Manuals & Data Analysis

Component	Specifications
siRNA plate	Cell Culture-ready Plate. 84 wells contain two siRNAs targeted against a single gene. 12 wells contain control siRNAs (positive, negative and transfection)
96 Sample RNA Isolation Kit	RNeasy® 96 Plates Elution Microtubes CL, racked Caps for Elution Microtubes in strips Buffer RLT Buffer RW1 Buffer RPE RNase-free water
HT First Strand Kit (included in the system)	GE2 (Genomic DNA Elimination Buffer) BC4 (RT Master mix) 96-well PCR Plate 12-well Strip TubesTube Aluminum Foil Sealing Films Compression mat

Storage Conditions

Please check the kit components immediately after you receive this package. SABiosciences is only responsible for missing items reported within two (2) business days of receipt.

The Biology-on-Array Systems are shipped in two boxes (Box 1 on Dry Ice and Box 2 at ambient conditions). Keep the siRNA plate, GE2 and BC4 at -20ºC for long-term storage.
The Systems are stable for six (6) months at the recommended temperature.
Do not use kit beyond the expiration date printed on the label.

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Functional Gene Grouping

Kit Components

How It Works

Manuals & Data Analysis

Overview of Biology-on-Array Protocol.

The Biology-on-Array is comprised of a siRNA plate, a HT first strand kit and data analysis software.

The siRNA plate is a cell culture grade 96-well plate having pre-dispended 84 siRNA pair (2 siRNA design per gene) targeting biologically-relevant groups of transcription regulators (transcription factors or epigenetic regulators) and important RNAi negative and positive controls.
The RNeasy® 96 Kit isolates total RNA from the 96 siRNA-treated samples.
The HT First Strand Kit synthesizes first strand cDNA from the 96 siRNA treated samples while eliminating genomic DNA in approximately 20 minutes.
The Excel-based data analysis software for Biology-on-Array performs the ΔΔCt based fold-change calculations from uploaded raw threshold cycle data from the gene-specific real time-PCR assay. The spreadsheet delivers results in a tabular format and assists in outlier identification and hit selection.

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