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Exons

Exons are the coding sequences within genes that are expressed as mature RNA.
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Most cited protocols related to «Exons»

1
BEDTools: Versatile Genomic Data Exploration
Table 1 illustrates the wide range of operations that BEDTools support. Many of the tools have extensive parameters that allow user-defined overlap criteria and fine control over how results are reported. Importantly, we have also defined a concise format (BEDPE) to facilitate comparisons of discontinuous features (e.g. paired-end sequence reads) to each other (pairToPair), and to genomic features in traditional BED format (pairToBed). This functionality is crucial for interpreting genomic rearrangements detected by paired-end mapping, and for identifying fusion genes or alternative splicing patterns by RNA-seq. To facilitate comparisons with data produced by current DNA sequencing technologies, intersectBed and pairToBed compute overlaps between sequence alignments in BAM format (Li et al., 2009 (link)), and a general purpose tool is provided to convert BAM alignments to BED format, thus facilitating the use of BAM alignments with all other BEDTools (Table 1). The following examples illustrate the use of intersectBed to isolate single nucleotide polymorphisms (SNPs) that overlap with genes, pairToBed to create a BAM file containing only those alignments that overlap with exons and intersectBed coupled with samtools to create a SAM file of alignments that do not intersect (-v) with repeats.

Summary of supported operations available in the BEDTools suite

UtilityDescription
intersectBed*Returns overlaps between two BED files.
pairToBedReturns overlaps between a BEDPE file and a BED file.
bamToBedConverts BAM alignments to BED or BEDPE format.
pairToPairReturns overlaps between two BEDPE files.
windowBedReturns overlaps between two BED files within a user-defined window.
closestBedReturns the closest feature to each entry in a BED file.
subtractBed*Removes the portion of an interval that is overlapped by another feature.
mergeBed*Merges overlapping features into a single feature.
coverageBed*Summarizes the depth and breadth of coverage of features in one BED file relative to another.
genomeCoverageBedHistogram or a ‘per base’ report of genome coverage.
fastaFromBedCreates FASTA sequences from BED intervals.
maskFastaFromBedMasks a FASTA file based upon BED coordinates.
shuffleBedPermutes the locations of features within a genome.
slopBedAdjusts features by a requested number of base pairs.
sortBedSorts BED files in useful ways.
linksBedCreates HTML links from a BED file.
complementBed*Returns intervals not spanned by features in a BED file.

Utilities in bold support sequence alignments in BAM. Utilities with an asterisk were compared with Galaxy and found to yield identical results.

Other notable tools include coverageBed, which calculates the depth and breadth of genomic coverage of one feature set (e.g. mapped sequence reads) relative to another; shuffleBed, which permutes the genomic positions of BED features to allow calculations of statistical enrichment; mergeBed, which combines overlapping features; and utilities that search for nearby yet non-overlapping features (closestBed and windowBed). BEDTools also includes utilities for extracting and masking FASTA sequences (Pearson and Lipman, 1988 (link)) based upon BED intervals. Tools with similar functionality to those provided by Galaxy were directly compared for correctness using the ‘knownGene’ and ‘RepeatMasker’ tracks from the hg19 build of the human genome. The results from all analogous tools were found to be identical (Table 1).
Quinlan A.R, & Hall I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841-842.
Publication 2010
Exons Gene Fusion Gene Rearrangement Genes Genome Genome, Human Sequence Alignment Single Nucleotide Polymorphism
2
Enhancing RNA-Seq Read Alignment Accuracy
Exon-spanning reads sometimes have very small anchors (defined here as 1–7 bp) in one of the exons. Correctly aligning these reads is extremely difficult because a 1- to 7-bp anchor will align to numerous locations, even in a local FM index. Arguably the most effective approach to align such short-anchored reads is to use splice site information to remove the introns computationally before alignment. We can identify and collect splice site locations when aligning reads with long anchors and then rerun HISAT for the short-anchored reads (Supplementary Fig. 9). This two-step approach is very similar to the two-step algorithm in TopHat2.
More specifically, in the two-step HISATx2 method, we use the first run of HISAT (HISATx1) to generate a list of splice sites supported by reads with long anchors. In the second run we then use the splice sites to align reads with small anchors. For example, consider the unmapped read spanning exons e2 and e3 (the upper portion of Supplementary Fig. 9). The right part of the read will be mapped to exon e3 using the global search and extension operations, leaving a short, 3-bp segment unmapped. We then check the splice sites found in the first run of HISAT to find any splice sites near this partial alignment. In this example, we find a splice site supported by a read spanning exons e2 and e3 with long anchors in each exon. On the basis of this information, we directly compare the 3 bp of the read and the corresponding genomic sequence in exon e2. If it matches, we combine the 3-bp alignment with the alignment of the rest of the read. This ‘junction extension’ procedure that makes use of previously identified splice sites is represented by brown arrows in the figure.
As we show in our experiments on simulated reads, this two-step strategy produces accurate alignment of reads with anchors as small as 1 bp (see Results). Although HISATx2 has considerably better sensitivity, it takes twice as long to run as HISATx1. As an alternative, we developed a hybrid method, HISAT, which has sensitivity almost equal to that of HISATx2 but with the speed of HISATx1. HISAT collects splice sites as it processes the reads, similarly to the first run of HISATx2. However, as it is processing, it uses the splice sites collected thus far to align short-anchored reads. In the vast majority of cases, it can align even the shortest anchors because it has seen the associated splice sites earlier. This result follows from the observation that most splice sites can be discovered within the first few million reads, and most RNA-seq data sets contain tens of millions of reads. As our results show, HISAT provides alignment sensitivity that very nearly matches the two-step HISATx2 algorithm, with a run time nearly as fast as the one-step HISAT method.
The hybrid approach is also effective in aligning reads spanning more than two exons, which are more likely to have small anchors. The alignment sensitivity for such reads increases from 53% using HISATx1 to 95% using HISAT (Supplementary Fig. 2).
Kim D., Langmead B, & Salzberg S.L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nature methods, 12(4), 357-360.
Publication 2015
Exons Genome Hybrids Hypersensitivity Introns RNA-Seq Toxic Epidermal Necrolysis Vision
3
Automated ANNOVAR Variant Annotation
While reading variants from input file, ANNOVAR scans the gene annotation database stored at local disk, and identifies intronic variants, exonic variants, intergenic variants, 5′/3′-UTR variants, splicing site variants and upstream/downstream variants (less than a threshold away from a transcript, by default 1 kb). For intergenic variants, the closest two genes and the distances to them are reported. For exonic variants, ANNOVAR scans annotated mRNA sequences to identify and report amino acid changes, as well as stop-gain or stop-loss mutations. ANNOVAR can also perform region-based annotations on many types of annotation tracks, such as the most conserved elements and the predicted transcription factor binding sites. These annotations must be downloaded by ANNOVAR, before they can be utilized. Finally, ANNOVAR can filter specific variants such as SNPs with >1% frequency in the 1000 Genomes Project, or non-synonymous SNPs with SIFT scores >0.05.
To automate the procedure of reducing large amounts of variants into a small subset of functionally important variants, a script (auto_annovar.pl) is provided in the ANNOVAR package. By default, auto_annovar.pl performs a multi-step procedure by executing ANNOVAR multiple times, each time with several different command line parameters, and generates a final output file containing the most likely causal variants and their corresponding candidate genes. For recessive diseases, this list can be further trimmed down to include genes with multiple variants that are predicted to be functionally important.
Wang K., Li M, & Hakonarson H. (2010). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38(16), e164.
Publication 2010
5' Untranslated Regions Amino Acids Binding Sites Exons Gene Annotation Genes Genetic Diversity Genome Introns Mutation Radionuclide Imaging RNA, Messenger Single Nucleotide Polymorphism Transcription Factor
4
Benchmarking Transcriptome Reconstruction Methods
Current gene annotations for S. pombe were downloaded as file ‘pombe_290110.gff’ from GeneDB (http://old.genedb.org/genedb/pombe/). RefSeq transcript gene annotations were downloaded for mouse at the UCSC mouse genome browser gateway (http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm9) in BED format. Protein coding nucleotide sequences were extracted from the genome sequences based on the gene annotations using custom PERL scripts. The mouse reference coding sequences were further distilled to remove entirely identical sequences corresponding to isoforms encoding identical proteins and paralogous sequences: the original 19,947 genes encoding 23,881 transcripts were reduced to 19,857 genes encoding 22,717 on-identical coding transcripts.
Reconstructed transcript sequences (via de novo assembly, Scripture, or Cufflinks) were mapped to the reference coding sequences using BLAT35 (link). Full-length reference annotation mappings were defined as having at least 95% sequence identity covering the entire reference coding sequence and containing at most 5% insertions or deletions (cumulative gap content). In evaluating methods that leverage the strand-specific data (Trinity and Cufflinks), proper sense-strand mapping of sequences was required. Transcripts reconstructed by the alternative methods (Scripture, ABySS, and SOAPdenovo) were allowed to map to either strand. Fusion transcripts were identified as individual reconstructed transcripts that mapped as full-length to multiple reference coding sequences and lacked overlap among the matching regions within the reconstructed transcript. One-to-one mappings were required between reconstructed transcripts and reference transcripts, including alternatively spliced isoforms, with the exception of fusion transcripts.
Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N, & Regev A. (2011). Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature biotechnology, 29(7), 644-652.
Publication 2011
Exons Gene Annotation Gene Deletion Genes Genome Insertion Mutation Mus Open Reading Frames Protein Isoforms Proteins
5
Benchmarking Transcriptome Reconstruction Methods
Current gene annotations for S. pombe were downloaded as file ‘pombe_290110.gff’ from GeneDB (http://old.genedb.org/genedb/pombe/). RefSeq transcript gene annotations were downloaded for mouse at the UCSC mouse genome browser gateway (http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm9) in BED format. Protein coding nucleotide sequences were extracted from the genome sequences based on the gene annotations using custom PERL scripts. The mouse reference coding sequences were further distilled to remove entirely identical sequences corresponding to isoforms encoding identical proteins and paralogous sequences: the original 19,947 genes encoding 23,881 transcripts were reduced to 19,857 genes encoding 22,717 on-identical coding transcripts.
Reconstructed transcript sequences (via de novo assembly, Scripture, or Cufflinks) were mapped to the reference coding sequences using BLAT35 (link). Full-length reference annotation mappings were defined as having at least 95% sequence identity covering the entire reference coding sequence and containing at most 5% insertions or deletions (cumulative gap content). In evaluating methods that leverage the strand-specific data (Trinity and Cufflinks), proper sense-strand mapping of sequences was required. Transcripts reconstructed by the alternative methods (Scripture, ABySS, and SOAPdenovo) were allowed to map to either strand. Fusion transcripts were identified as individual reconstructed transcripts that mapped as full-length to multiple reference coding sequences and lacked overlap among the matching regions within the reconstructed transcript. One-to-one mappings were required between reconstructed transcripts and reference transcripts, including alternatively spliced isoforms, with the exception of fusion transcripts.
Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N, & Regev A. (2011). Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature biotechnology, 29(7), 644-652.
Publication 2011
Exons Gene Annotation Gene Deletion Genes Genome Insertion Mutation Mus Open Reading Frames Protein Isoforms Proteins

Most recents protocols related to «Exons»

1
Micropeptides Identified from lncRNAs
Not available on PMC !

Example 1

The authors of the invention have identified 3 micropeptides corresponding to sequences SEQ ID NO: 1, 2 and 3.

The micropeptide of SEQ ID NO 1 is a highly conserved 87 aa micropeptide whose sequence is:

(FIG. 1A)
MEGLRRGLSRWKRYHIKVHLADEALLLPLTVRPRDTLSDLRAQLVGQGVSS
WKRAFYYNARRLDDHQTVRDARLQDGSVLLLVSDPR.

In silico analysis of the amino acid sequence predicts a 3D structure resembling the protein UBIQUITIN (FIG. 1B). SEQ ID NO 1 micropeptide is coded by the lncRNA TINCR (LINC00036 in humans and Gm20219 in mice).

The micropeptide of SEQ ID NO: 2 is a 64-amino acid micropeptide whose sequence is:

(FIG. 2A)
MVRRKSMKKPRSVGEKKVEAKKQLPEQTVQKPRQECREAGPLFLQSRRETR
DPETRATYLCGEG.

It is encoded by ZEB2 antisense 1 (ZEB2AS1) long non-coding RNA (lncRNA). ZEB2AS1 is a natural antisense transcript corresponding to the 5′ untranslated region (UTR) of zinc finger E-box binding homeobox 2 (ZEB2). The ORF encoding the micropeptide spams part of the second and third exons of the lncRNA. I-Tasser, a 3D protein structure predictor, has been used in order to build a model of SEQ ID NO: 2 micropeptide 3D structure (FIG. 2B). Further in-silico analysis has revealed high amino acidic sequence conservation across the species and a potential cytoplasmatic localization of the micropeptide of SEQ ID NO: 2.

The micropeptide of SEQ ID NO: 3 is a 78-amino acid micropeptide encoded by the first exon of LINC0086 lncRNA. Its sequence, highly conserved across evolution is:

(FIG. 3A)
MAASAALSAAAAAAALSGLAVRLSRSAAARGSYGAFCKGLTRTLLTFFDLA
WRLRMNFPYFYIVASVMLNVRLQVRIE.

In silico analysis of this sequence predicted a tertiary structure (FIG. 3B) with a transmembrane domain at C-terminal of the protein and a signal peptide in the first 25 amino acids.

US11858972B2. Micropeptides and uses thereof (2024-01-02). FUNDACIÓ PRIVADA INSTITUT D'INVESTIGACIÓ ONCOLÒGICA DE VALL HEBRON [ES]. Inventors: Maria Abad Méndez [ES], Olga Boix Sánchez [ES], Emanuela Greco [ES], Iñaki Merino Valverde [ES].
Full text: Click here
Patent 2024
Amino Acids Amino Acid Sequence Biological Evolution Cytoplasm Exons Homo sapiens Integral Membrane Proteins Mice, House Protein Domain Proteins RNA, Long Untranslated Sequence Analysis Sequence Analysis, Protein Signal Peptides Ubiquitin Zinc Finger E-box Binding Homeobox 2
2
CH25H Knockout Reduces Alzheimer's Pathology
Not available on PMC !

Example 5

We studied the effect of CH25H KO in AD pathogenesis. SgRNAs targeting CH25H were designed with sgRNA1 being SEQ ID NO: 1 and sg RNA2 being SEQ ID NO: 2. See FIGS. 12A and 12B. With the two sg RNAs, CH25H gene were knocked out by crisper/cas9 method so that 46 base pairs (bp) were deleted in the exon of CH25H genes (see FIG. 12C), resulting in CH25H knockout (KO) mice.

In the CH25H KO mice, the deletion of the 46 bp fragment of CH25H gene was detected with the 488 bp band being the deleted CH25H gene and the 534 bp being the wild-type gene. The expression of CH25H mRNA in the CH25H KO mice was significantly reduced (FIG. 12E).

Once crossed to 5XFAD mice, the CH25H KO showed similar phenotype to STAT1 KO. Aβ was greatly reduced in both immunostaining and Elisa quantification (FIGS. 13A, 13B and 13C, respectively). Conversely, mice injected with 25-OHC had significant high amount of Aβ (FIGS. 11A, 11B and 11C).

To test the effect of reduced Aβ on cognitive abilities, the mice were examined by watermaze. 5XFAD mice gradually learned to locate the platform underneath the water, while the CH25H KO mice took significantly (p<0.05) less time to find the platform, indicating they performed better in learning and memory task (FIG. 14).

US11873321B2. Compositions and methods for treating alzheimer's disease (2024-01-16). Generos Biopharma Ltd. [CN]. Inventors: Xin-Yuan Fu [US], Yi Zhou [SG].
Full text: Click here
Patent 2024
Cognition Deletion Mutation Enzyme-Linked Immunosorbent Assay Exons Genes Memory Mice, Knockout Mice, Laboratory pathogenesis Phenotype RNA RNA, Messenger STAT1 protein, human
3
Monitoring Duchenne Muscular Dystrophy Exon Skipping
Not available on PMC !

Example 4

ASOs also are being evaluated therapeutically for another form of muscle disease, Duchenne muscular dystrophy (DMD), to modify dystrophin pre-mRNA splicing directly by inducing skipping of a target exon to restore the open reading frame and produce a truncated, partially functional protein27, 28. Detection of therapeutic drug effects in DMD patients involves multiple muscle biopsies to examine splicing outcomes and dystrophin protein production. To test whether biofluid exRNA contains DMD deletion transcripts, we examined urine from several subjects with DMD and found patient-specific DMD deletion transcripts (FIGS. 6A and B), suggesting this biofluid exRNA is a viable approach to monitor therapeutic exon-skipping ASO drug effects in DMD patients as personalized genetic markers27, 28.

US11866783B2. Extracellular mRNA markers of muscular dystrophies in human urine (2024-01-09). The General Hospital Corporation [US]. Inventors: Thurman Wheeler [US], Xandra O. Breakefield [US], Leonora Balaj [US].
Full text: Click here
Patent 2024
Biopsy Deletion Mutation Exons Figs Homo sapiens mRNA Precursor Muscle Tissue Muscular Dystrophy, Duchenne Myopathy Patients Pharmaceutical Preparations Proteins Substance Abuse Detection Therapeutic Effect Therapeutics Urine
4
CRISPR-Mediated Mutation Correction and Knock-In for G6PC Gene
Not available on PMC !

Example 94

After testing the gRNAs for both on-target activity and off-target activity, the mutation correction and knock-in strategies will be tested for HDR gene editing.

For the mutation correction approach, the donor DNA template will be provided as a short single-stranded oligonucleotide, a short double-stranded oligonucleotide (PAM sequence intact/PAM sequence mutated), a long single-stranded DNA molecule (PAM sequence intact/PAM sequence mutated) or a long double-stranded DNA molecule (PAM sequence intact/PAM sequence mutated). In addition, the donor DNA template will be delivered by AAV.

For the cDNA knock-in approach, a single-stranded or double-stranded DNA having homologous arms to the 17q21 region may include more than 40 nt of the first exon (the first coding exon) of the G6PC gene, the complete CDS of the G6PC gene and 3′UTR of the G6PC gene, and at least 40 nt of the following intron. The single-stranded or double-stranded DNA having homologous arms to the 17q21 region, which includes more than 80 nt of the first exon of the G6PC gene, the complete CDS of the G6PC gene and 3′UTR of the G6PC gene, and at least 80 nt of the following intron. The single-stranded or double-stranded DNA having homologous arms to the 17q21 region may include more than 100 nt of the first exon of the G6PC gene, the complete CDS of the G6PC gene and 3′UTR of the G6PC gene, and at least 100 nt of the following intron. The single-stranded or double-stranded DNA having homologous arms to the 17q21 region may include more than 150 nt of the first exon of the G6PC gene, the complete CDS of the G6PC gene and 3′UTR of the G6PC gene, and at least 150 nt of the following intron. The single-stranded or double-stranded DNA having homologous arms to the 17q21 region may include more than 300 nt of the first exon of the G6PC gene, the complete CDS of the G6PC gene and 3′UTR of the G6PC gene, and at least 300 nt of the following intron. The single-stranded or double-stranded DNA having homologous arms to the 17q21 region may include more than 400 nt of the first exon of the G6PC gene, the complete CDS of the G6PC gene and 3′UTR of the G6PC gene, and at least 400 nt of the following the first intron. Alternatively, the DNA template will be delivered by AAV.

Next, the efficiency of HDR mediated correction of the common mutation of G6PC R83 and knock-in of cDNA into the 1st exon will be assessed.

US11866727B2. Materials and methods for treatment of glycogen storage disease type 1A (2024-01-09). CRISPR THERAPEUTICS AG [None]. Inventors: Chad Albert Cowan [US], Roman Lvovitch Bogorad [US], Ante Sven Lundberg [US], Kirsten Leah Beaudry [US].
Full text: Click here
Patent 2024
3' Untranslated Regions Arm, Upper DNA, Complementary DNA, Double-Stranded Exons Genes Introns Mutation Oligonucleotides Tissue Donors
5
Identifying Optimal miR Expression Enhancers
Not available on PMC !

Example 2

MiRs are usually expressed from individual Pol II promoters and/or are excised out of introns, with many exceptions such as miRs generated in exons. To identify the agents that can increase selected miRs levels most effectively, expression plasmids in which GFP/Luc are expressed from miRs promoters are generated.

The enhancement of miR expression is engineered separately for each selected miR. Luciferase and GFP co-expression constructs with different miR promoter lengths are generated (usually, four for each miR). Stably transfected cells with each of the promoter constructs are then generated. This system allows the high-throughput identification of the preferred agent that enhances each miR's expression. Based on this HTP screening the best hits (usually, 10 hits, based on a readout of GFP/Luc highest expression) are identified. The effect of the identified agents is then tested by performing both a dose escalation and kinetic experiments. The agents exhibiting the lowest effective concentrations (usually 5 candidates) are used in further experiments.

US11865090B2. Tumor suppressive microRNAs for cancer therapy (2024-01-09). Hadasit Medical Research Services and Development Ltd. [IL]. Inventors: Eithan Galun [IL], Hilla Giladi [IL], Chofit Chai [IL], Nofar Rosenberg [IL], Dayana Yaish [IL], Zohar Shmuelian [IL].
Full text: Click here
Patent 2024
Cells Exons Introns Kinetics Luciferases Plasmids RNA Polymerase II

Top products related to «Exons»

1
Hiseq 2000 by Illumina
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The HiSeq 2000 is a high-throughput DNA sequencing system designed by Illumina. It utilizes sequencing-by-synthesis technology to generate large volumes of sequence data. The HiSeq 2000 is capable of producing up to 600 gigabases of sequence data per run.
2
Trizol reagent by Thermo Fisher Scientific
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
3
Rneasy mini kit by Qiagen
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The RNeasy Mini Kit is a laboratory equipment designed for the purification of total RNA from a variety of sample types, including animal cells, tissues, and other biological materials. The kit utilizes a silica-based membrane technology to selectively bind and isolate RNA molecules, allowing for efficient extraction and recovery of high-quality RNA.
4
Hiseq 2500 by Illumina
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The HiSeq 2500 is a high-throughput DNA sequencing system designed for a wide range of applications, including whole-genome sequencing, targeted sequencing, and transcriptome analysis. The system utilizes Illumina's proprietary sequencing-by-synthesis technology to generate high-quality sequencing data with speed and accuracy.
5
Trizol by Thermo Fisher Scientific
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TRIzol is a monophasic solution of phenol and guanidine isothiocyanate that is used for the isolation of total RNA from various biological samples. It is a reagent designed to facilitate the disruption of cells and the subsequent isolation of RNA.
6
Lipofectamine 2000 by Thermo Fisher Scientific
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Lipofectamine 2000 is a cationic lipid-based transfection reagent designed for efficient and reliable delivery of nucleic acids, such as plasmid DNA and small interfering RNA (siRNA), into a wide range of eukaryotic cell types. It facilitates the formation of complexes between the nucleic acid and the lipid components, which can then be introduced into cells to enable gene expression or gene silencing studies.
7
Bigdye terminator v3.1 cycle sequencing kit by Thermo Fisher Scientific
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The BigDye Terminator v3.1 Cycle Sequencing Kit is a reagent kit used for DNA sequencing. It contains the necessary components, including fluorescently labeled dideoxynucleotides, to perform the Sanger sequencing method.
8
Qiaamp dna mini kit by Qiagen
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The QIAamp DNA Mini Kit is a laboratory equipment product designed for the purification of genomic DNA from a variety of sample types. It utilizes a silica-membrane-based technology to efficiently capture and purify DNA, which can then be used for various downstream applications.
9
High capacity cdna reverse transcription kit by Thermo Fisher Scientific
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The High-Capacity cDNA Reverse Transcription Kit is a laboratory tool used to convert RNA into complementary DNA (cDNA) molecules. It provides a reliable and efficient method for performing reverse transcription, a fundamental step in various molecular biology applications.
10
Novaseq 6000 by Illumina
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The NovaSeq 6000 is a high-throughput sequencing system designed for large-scale genomic projects. It utilizes Illumina's sequencing by synthesis (SBS) technology to generate high-quality sequencing data. The NovaSeq 6000 can process multiple samples simultaneously and is capable of producing up to 6 Tb of data per run, making it suitable for a wide range of applications, including whole-genome sequencing, exome sequencing, and RNA sequencing.

More about "Exons"

Exons are the essential coding sequences within genes that are expressed as mature RNA, playing a crucial role in gene expression and protein synthesis.
These genetic elements have been extensively studied using various techniques and technologies.
Researchers have utilized platforms like the HiSeq 2000, HiSeq 2500, and NovaSeq 6000 to sequence and analyze exons, gaining insights into their structure, function, and expression patterns.
The isolation and purification of RNA, a crucial step in exon research, often involve the use of reagents such as TRIzol and the RNeasy Mini Kit.
These tools help extract and purify high-quality RNA, including the mature transcripts containing exons.
Reverse transcription, facilitated by the High-Capacity cDNA Reverse Transcription Kit, then converts the RNA into complementary DNA (cDNA) for further analysis.
Downstream processes, such as sequencing, often employ methods like the BigDye Terminator v3.1 Cycle Sequencing Kit to determine the nucleotide sequence of the exons.
Additionally, the QIAamp DNA Mini Kit is commonly used to isolate and purify genomic DNA, which can be utilized to study the genomic context and organization of exons.
In the field of gene expression and regulation, transfection reagents like Lipofectamine 2000 have been used to introduce genetic material, including exon-containing constructs, into cells, enabling the study of exon function and splicing.
By leveraging these advanced techniques and technologies, researchers can unlock deeper insights into the structure, expression, and regulation of exons, leading to a better understanding of gene function and the development of novel therapeutic approaches targeting this crucial genetic element.