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Several days sgo,I have read a newspaper, the scientists dissected human breast epithelial cells and identified three epithelial cell populations. The discovery of these new cells helps redefine the origin of breast cancer, improve early cancer detection, slow cancer progression, and possibly even prevent cancer.In this study, the researchers utilized a next-generation sequencing technology combined with single cell RNA sequencing (Single cell RNA seq) to create a high-resolution molecular screening of human breast epithelial cells. Single-cell RNAseq technology has led to the discovery of cellular differences that have not been previously discovered.
Breast cancer arises from the breast epithelium. Breast cancer arises from genetic variation of breast epithelial cells. Genetic changes cause cancer cells of the breast tissue to produce canceration. Understanding the early origin of breast cancer has the potential to be transformed into an early diagnosis method for cancer, and to build a first line of defense against cancer before the disease threatens life. I hope that this technology could be used for cancer research, more information on the web:https://www.cd-genomics.com/single-cell-rna-sequencing.html
ICH S7B guideline1 regulates in vitro IKr assay (such as hERG safety assay) and in vitro QT assay for identifying and assessing the potential of a test compound to delay ventricular repolarization. Ventricular repolarization is a complex physiological process determined by the duration of the cardiac action potential. It is the net result of the activities of many highly interdependent membrane ion channels and transporters. Many compounds can affect the activities of the ion channels or transporters, thus have the potential of delaying the ventricular repolarization and leading to prolonged QT interval.

https://www.creative-bioarray.com/Services/hERG-Safety.htm
Hello
I would like to access the potato annotation file in iTAG nomenclature with their respective TAIR nomenclature codes equivalent to each gene. Is that possible? I can not find the annotation file that includes that information. I need to match the nomenclature accepted in DAVID (The Database for Annotation).

Example in PGSC annotation available in Phytozome

PGSC0003DMG400000001 = AT1G12600.1
Dear Sol genomics network,

Shin-Han Shiu, Marja Timmermans, and I are organizing this summer's Cold Spring Harbor "Frontiers and Techniques in Plant Sciences" (June 27 - July 17).

The course provides foundational work in plant sciences as well as practical laboratory experience in techniques like RNA-seq, proteomics, mapping-by-sequencing, genome editing, and imaging. In recent years the course has stressed the quantitative nature of plant biology and students will be introduced to computational techniques required for analyzing large datasets.

As you may know, this course has been going strong for >30 years and has been taken by many successful plant scientists. I encourage you to let students, postdocs and faculty colleagues know about the course, which will be taught be a fantastic group of investigators http://meetings.cshl.edu/courses/2014/c-plan14.shtml.

CSH can provide limited financial support for US students to cover their tuition room and board through an NSF grant and other sources of funding. Thus, I strongly encourage you to consider sending your new students and/or post-docs to the course, which has had a very strong positive impact on the trajectory of participants.

APPLICATIONS ARE DUE APRIL 15.

Thank you,

Mark Johnson
Brown University

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Is it safe to directly map the gene identifiers (Solyc00g005000.2) using the primary id (Solyc00g005000)?
Transitions are base mutations of purine to purine (A <-> G) or pyrimidine to pyrimidine (C <-> T). Transversions are purine to pyrimidine or vice versa (A <-> C, A <-> T, G <-> C, G <-> T). And it is well-known that transitions are more common than transversions in the populations.

So what is the condition in the evolution of duplicated genes? Suppose a gene A is duplicated with two copies A1 and A2 in the same genome (not two alleles in different sets of chromosomes, or the same gene in two different cells/organisms). At first A1 and A2 had the same sequence, but then they went through an evolution process and each got some mutations. Now let's check the sequence of A1 and A2 again, are the differences between A1 and A2 mainly transitions instead of transversions?

Although I think it would not be surprising to find that transitions are more common in this condition, I've searched some papers focusing on the evolution of duplicated genes to look for some support. However, they mainly discuss what happened to their functions instead of sequences. https://www.sprakdesign.com/
Creative Bioarray cDNA can be used in gene expression and cloning studies, gene mutation analysis, analysis of mRNA alternative splicing and other molecular biology fields.

https://www.creative-bioarray.com/products/cdna-199.htm
What is a genome?
A genome is a complete deoxyribonucleic acid (DNA) of an organism, a compound containing genetic instructions needed to develop and direct each biological activity. A DNA molecule consists of two twisting, paired strands. Each strand consists of four chemical units called nucleotide bases. The bases are adenine (A), thymine (T), guanine (G) and cytosine (C). The basis of the opposite strand is specific; A is always paired with T, and C is always paired with G.

The human genome contains approximately 3 billion of these base pairs, which are located in 23 pairs of chromosomes in the nucleus of our cells. Each chromosome contains hundreds to thousands of genes with instructions for making proteins. Each of the estimated 30,000 genes in the human genome produces an average of three proteins.
What is Human Genome Sequencing and how to sequence the genome?
Human Genome Sequencing, which means determining the exact sequence of base pairs in a DNA fragment. Human chromosomes range in size from about 50,000,000 to 300,000,000 base pairs. Because bases exist in pairs, and the identity of one base in the pair determines another member of the pair, scientists don’t have to report the two bases of the pair.
More on the https://www.cd-genomics.com/Human-Whole-Genome-PacBio-SMRT-Sequencing.html
Hi dears,
Is there any possibility that someone can share the cDNA library of benthamiana? Please let me know, if it is possible. Thanks.
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Started by:
Peng Wang

 
Here we report a serious problem with tobacco gene models. We tried to map the gene models of Nitociana tabacum (TN90), which you provide in your ftp, to the TN90 genome assembly sequences. Unfortunately, a lot of gene models could not be mapped. Of the 122388 gene models you provided in the gene model file,only 53714 could be mapped to the genome assembly. We do not know what method you used to identify gene models. Could you check all the datasets of the three tobacco varieties(TN90, K326 and Bathma)? Thank you.
Creative Bioarray maintains various human and animal <a href="https://www.creative-bioarray.com/products/tumor-cell-types-13.htm">tumor cell</a> lines that are invaluable for medical, scientific and pharmaceutical institutions. Creative Bioarray consistently attains the highest standards and uses the most reliable procedures to verify every cell line.

Every study is different and requires different cells and samples. Creative Bioarray has the largest selection of organ-specific and cancer-related tumor cells available. Every sample has its own description and origin included so you know exactly what you are receiving with us.
Lipidomics is a study of composition and quantification of lipids at a systematic level, so as to uncover the interactions between lipids and other macromolecules, and the mechanisms of lipids in regulating biological activities. At present, LC-MS and shotgun lipidomics are two mainstream technology for lipidomics analysis. LC-MS utilizes high-throughput liquid chromatography system to separate lipids based on their physical and chemical properties, followed by mass spectrometry analysis. Whereas, shotgun lipidomics is independent of liquid chromatography technology, and separates lipids through intrasource separation system, which adjusts pH value of solution and changes the ionization status of lipids, followed by direct infusion into mass spectrometer for lipids identification.

LC-MS is a powerful tool for discovery lipidomics, as LC-MS usually achieves detection of lipids at ppm level and accurate analysis of lipids side chains through MS2 fragmentation. Whereas, shotgun lipidomics is more widely used for (semi)-quantitation of targeted lipids. Reference: http://www.mtoz-biolabs.com/lipidomics.htm
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I would like to know whether Triticum aestivum database is updated and is there any reference where I researchers have designed construct for VIGS in wheat
Several days sgo,I have read a newspaper, the scientists dissected human breast epithelial cells and identified three epithelial cell populations. The discovery of these new cells helps redefine the origin of breast cancer, improve early cancer detection, slow cancer progression, and possibly even prevent cancer.In this study, the researchers utilized a next-generation sequencing technology combined with single cell RNA sequencing (Single cell RNA seq) to create a high-resolution molecular screening of human breast epithelial cells. Single-cell RNAseq technology has led to the discovery of cellular differences that have not been previously discovered.
Breast cancer arises from the breast epithelium. Breast cancer arises from genetic variation of breast epithelial cells. Genetic changes cause cancer cells of the breast tissue to produce canceration. Understanding the early origin of breast cancer has the potential to be transformed into an early diagnosis method for cancer, and to build a first line of defense against cancer before the disease threatens life. I hope that this technology could be used for cancer research, more information on the web:https://www.cd-genomics.com/single-cell-rna-sequencing.html
Dears friends: I want to Know if Are there microsatellite or other molecular marker that can be used for identify differents species in tomato??? i mean between sculentum and
Creative Bioarray maintains various human and animal <a href="https://www.creative-bioarray.com/products/tumor-cell-types-13.htm">tumor cell</a> lines that are invaluable for medical, scientific and pharmaceutical institutions. Creative Bioarray consistently attains the highest standards and uses the most reliable procedures to verify every cell line.

Every study is different and requires different cells and samples. Creative Bioarray has the largest selection of organ-specific and cancer-related tumor cells available. Every sample has its own description and origin included so you know exactly what you are receiving with us.
Dear friends, I am about to begin an investigation of lycopene content in tomato species, as well as identification of microsatellites to identify the gene or genes responsible for the character under study, so I ask if I could help with information on the research topic . Thank you very much
I have a list of tomato gene model ids. I would like to know how can I map tomato gene model ids (for ex, Solyc09g009710.2) to Affymetrix GeneChip Tomato Genome Array (for ex, Les.4492.2.S1_at)?
Where Can I get the mapping file?

In FAQ, I found a mapping file, but it is ITAG model to SGN.
Dear All,

I would like to work on phenotyping tomato and brinjal (egg plant) for abiotic stress tolerance traits. For that I would like to know what are the materials and methods needed.

Why I am asking is that if any one in the community had developed a set of protocols for low cost phenotyoing, i would like to use it.

Please connect me with people who are working on phenotyping tomato.

Thanks
Sridhar
What is a genome?
A genome is a complete deoxyribonucleic acid (DNA) of an organism, a compound containing genetic instructions needed to develop and direct each biological activity. A DNA molecule consists of two twisting, paired strands. Each strand consists of four chemical units called nucleotide bases. The bases are adenine (A), thymine (T), guanine (G) and cytosine (C). The basis of the opposite strand is specific; A is always paired with T, and C is always paired with G.

The human genome contains approximately 3 billion of these base pairs, which are located in 23 pairs of chromosomes in the nucleus of our cells. Each chromosome contains hundreds to thousands of genes with instructions for making proteins. Each of the estimated 30,000 genes in the human genome produces an average of three proteins.
What is Human Genome Sequencing and how to sequence the genome?
Human Genome Sequencing, which means determining the exact sequence of base pairs in a DNA fragment. Human chromosomes range in size from about 50,000,000 to 300,000,000 base pairs. Because bases exist in pairs, and the identity of one base in the pair determines another member of the pair, scientists don’t have to report the two bases of the pair.
More on the https://www.cd-genomics.com/Human-Whole-Genome-PacBio-SMRT-Sequencing.html
Started by:
Naama Menda
2018-09-28 12:20:26
 
This topic discusses issues in developing controlled-vocabularies for describing Solanaceae phenotypes and traits.
Most should be covered by the 'Solanaceae Phenotype Ontology' (SPO)
(see SGN->Tools->Ontology browser) which is growing by demand of its users community.
Terms which exist in other ontologies (PO, PATO, etc) are mapped to SPO terms.
In some cases it will be advised to use other vocabularies, instead of providing new SPO terms.
Started by:
john binns
2018-01-09 05:45:44
 
This topic is for members of the SOL community from around the world to publish job openings. If interested, please reply directly to the poster. Job postings submitters please note that the postings will be removed by default 8 months after posting.
Hi, I would like to know if there is a straightforward way to translate the one nomenclature to the other.
Both refer to genes/loci/protein, right... but if I have to compare to see coincidences from one list in one format and one list in the other (having hundreds of proteins/genes in each list), I can die doing searches and endless alignments, and still not accomplishing the job...
Please help.
Thank you very much.
Started by:
Emilio Ortiz
2014-01-19 23:11:32
 
Hi,

Is there any way to download the 2860 COSII sequences? Please let me know.


Thank you,
Started by:
Lukas Mueller
2013-02-20 23:31:36
 
This topic contains release notes for new SGN data releases.
Started by:
Lukas Mueller
2011-12-14 10:49:32
 
In the next few years, hundreds of Solanaceae will be sequenced using next generation sequencing methods. If you intend to sequence a Solanaceae, please provide information on the species to avoid duplicate sequencing of accessions on the SGN SOL-100 page http://solgenomics.net/organism/sol100/view. This topic is for the discussion of SOL-100 related questions.
This topics is for the researchers of the SOL community around the world who need some specific materials for their experiments and express some request to those who could provide them with the expected materials or resources.
Started by:
Lukas Mueller
2009-07-23 12:10:22
 
This topic contains release notes for new SGN website features.