scholarly journals Preparing and Analyzing Expressed Sequence Tags (ESTs) Library for the Mammary Tissue of Local Turkish Kivircik Sheep

2017 ◽  
Vol 2017 ◽  
pp. 1-14
Author(s):  
Nehir Ozdemir Ozgenturk ◽  
Zehra Omeroglu Ulu ◽  
Salih Ulu ◽  
Cemal Un ◽  
Kemal Ozdem Oztabak ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expressed Sequence Tags ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cdna Libraries ◽  
Mammary Tissue ◽  
Mammary Gland Tissue ◽  
Gland Tissue ◽  
Source Of Information ◽  
Expressed Sequence

Kivircik sheep is an important local Turkish sheep according to its meat quality and milk productivity. The aim of this study was to analyze gene expression profiles of both prenatal and postnatal stages for the Kivircik sheep. Therefore, two different cDNA libraries, which were taken from the same Kivircik sheep mammary gland tissue at prenatal and postnatal stages, were constructed. Total 3072 colonies which were randomly selected from the two libraries were sequenced for developing a sheep ESTs collection. We used Phred/Phrap computer programs for analysis of the raw EST and readable EST sequences were assembled with the CAP3 software. Putative functions of all unique sequences and statistical analysis were determined by Geneious software. Total 422 ESTs have over 80% similarity to known sequences of other organisms in NCBI classified by Panther database for the Gene Ontology (GO) category. By comparing gene expression profiles, we observed some putative genes that may be relative to reproductive performance or play important roles in milk synthesis and secretion. A total of 2414 ESTs have been deposited to the NCBI GenBank database (GW996847–GW999260). EST data in this study have provided a new source of information to functional genome studies of sheep.

scholarly journals Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivum L.)

Genome ◽  
2006 ◽  
Vol 49 (5) ◽  
pp. 531-544 ◽  
Author(s):  
S Chao ◽  
G R Lazo ◽  
F You ◽  
C C Crossman ◽  
D D Hummel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Triticum Aestivum ◽  
Expressed Sequence Tag ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Tetraploid Wheat ◽  
Gene Expression Profiles ◽  
Triticum Aestivum L ◽  
Cdna Libraries ◽  
Expressed Sequence

The US Wheat Genome Project, funded by the National Science Foundation, developed the first large public Triticeae expressed sequence tag (EST) resource. Altogether, 116 272 ESTs were produced, comprising 100 674 5′ ESTs and 15 598 3′ ESTs. These ESTs were derived from 42 cDNA libraries, which were created from hexaploid bread wheat (Triticum aestivum L.) and its close relatives, including diploid wheat (T. monococcum L. and Aegilops speltoides L.), tetraploid wheat (T. turgidum L.), and rye (Secale cereale L.), using tissues collected from various stages of plant growth and development and under diverse regimes of abiotic and biotic stress treatments. ESTs were assembled into 18 876 contigs and 23 034 singletons, or 41 910 wheat unigenes. Over 90% of the contigs contained fewer than 10 EST members, implying that the ESTs represented a diverse selection of genes and that genes expressed at low and moderate to high levels were well sampled. Statistical methods were used to study the correlation of gene expression patterns, based on the ESTs clustered in the1536 contigs that contained at least 10 5′ EST members and thus representing the most abundant genes expressed in wheat. Analysis further identified genes in wheat that were significantly upregulated (p < 0.05) in tissues under various abiotic stresses when compared with control tissues. Though the function annotation cannot be assigned for many of these genes, it is likely that they play a role associated with the stress response. This study predicted the possible functionality for 4% of total wheat unigenes, which leaves the remaining 96% with their functional roles and expression patterns largely unknown. Nonetheless, the EST data generated in this project provide a diverse and rich source for gene discovery in wheat.Key words: Expressed sequence tags, ESTs, gene expression profiles, wheat, Triticeae.

scholarly journals Tandem arrayed Iigation of expressed sequence tags (TALEST): a new method for generating global gene expression profiles

1999 ◽  
Vol 27 (18) ◽  
pp. i-viii
Author(s):  
D. G. Spinella ◽  
A. K. Bernardino ◽  
A. C. Redding ◽  
P. Koutz ◽  
Y. Wei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expressed Sequence Tags ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
New Method ◽  
Expressed Sequence

scholarly journals Analysis of Expressed Sequence Tag Data and Gene Expression Profiles Involved in Conidial Germination of Fusarium oxysporum

2006 ◽  
Vol 72 (2) ◽  
pp. 1667-1671 ◽  
Author(s):  
Ye Deng ◽  
Haitao Dong ◽  
Qingchao Jin ◽  
Cheng'en Dai ◽  
Yongqi Fang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Fusarium Oxysporum ◽  
Cdna Library ◽  
Expressed Sequence Tag ◽  
Expression Profiles ◽  
Cdna Array ◽  
Gene Expression Profiles ◽  
Conidial Germination ◽  
Expressed Sequence

ABSTRACT We obtained 3,372 tentative unique transcripts (TUTs) from a cDNA library of Fusarium oxysporum. A cDNA array with 3,158 TUTs was produced to analyze gene expression profiles in conidial germination. It seems that ras and other signaling genes, e.g., ccg, cooperatively initiate conidial germination in Fusarium by increasing protein synthesis.

scholarly journals Quantitative Gene Expression Profiles in Real Time From Expressed Sequence Tag Databases

2010 ◽  
Vol 14 (6) ◽  
pp. 321-336 ◽  
Author(s):  
VINCENT A. FUNARI ◽  
KONSTANTIN VOEVODSKI ◽  
DIMITRY LEYFER ◽  
LAURA YERKES ◽  
DONALD CRAMER ◽  
...  
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Expressed Sequence Tag ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Quantitative Gene Expression ◽  
Expressed Sequence

scholarly journals RNA-seq Analysis Reveals Gene Expression Profiling of Female Fertile and Sterile Ovules of Pinus Tabulaeformis Carr. during Free Nuclear Mitosis of the Female Gametophyte

2018 ◽  
Vol 19 (8) ◽  
pp. 2246 ◽  
Author(s):  
Yang Yao ◽  
Rui Han ◽  
Zaixin Gong ◽  
Caixia Zheng ◽  
Yuanyuan Zhao
Keyword(s):  
Gene Expression ◽  
Female Gametophyte ◽  
Expression Profiles ◽  
Signal Transduction Pathway ◽  
Gene Expression Profiles ◽  
Pinus Tabulaeformis ◽  
Cdna Libraries ◽  
Pcr Analysis ◽  
Transcriptional Networks ◽  
Ovule Development

The development of the female gametophyte (FG) is one of the key processes of life cycle alteration between the haploid gametophyte and the diploid sporophytes in plants and it is required for successful seed development after fertilization. It is well demonstrated that free nuclear mitosis (FNM) of FG is crucial for the development of the ovule. However, studies of the molecular mechanism of ovule and FG development focused mainly on angiosperms, such as Arabidopsis thaliana and further investigation of gymnosperms remains to be completed. Here, Illumina sequencing of six transcriptomic libraries obtained from developing and abortive ovules at different stages during free nuclear mitosis of magagametophyte (FNMM) was used to acquire transcriptome data and gene expression profiles of Pinus tabulaeformis. Six cDNA libraries generated a total of 71.0 million high-quality clean reads that aligned with 63,449 unigenes and the comparison between developing and abortive ovules identified 7174 differentially expressed genes (DEGs). From the functional annotation results, DEGs involved in the cell cycle and phytohormone regulation were highlighted to reveal their biological importance in ovule development. Furthermore, validation of DEGs from the phytohormone signal transduction pathway was performed using quantitative real-time PCR analysis, revealing the dynamics of transcriptional networks and potential key components in the regulation of FG development in P. tabulaeformis were identified. These findings provide new insights into the regulatory mechanisms of ovule development in woody gymnosperms.

Bovine mammary gene expression profiling using a cDNA microarray enhanced for mammary-specific transcripts

2003 ◽  
Vol 16 (1) ◽  
pp. 8-18 ◽  
Author(s):  
Steven P. Suchyta ◽  
Sue Sipkovsky ◽  
Robert G. Halgren ◽  
Rachael Kruska ◽  
Michael Elftman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mammary Gland ◽  
Cdna Microarray ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Mammary Tissue ◽  
Cell Cycle Regulators ◽  
Bovine Mammary Gland ◽  
Pilot Studies

A cDNA microarray resource enhanced for transcripts specific to the bovine mammary gland (BMAM) has been developed and used in pilot studies to examine gene expression profiles in the mammary gland. One goal driving development of this resource was to shed some light on the pathways and mechanisms specifically related to bovine mammary gland growth and development. To accomplish this, gene expression patterns from bovine adipose, liver, adrenal, lymph, spleen, thymus, gut, and developing mammary tissue were compared using the BMAM microarray. We have thus identified a putative set of 16 genes being preferentially expressed in developing mammary gland. Another of our long-term goals is to elucidate the genes and pathways associated with bovine lactation and involution and to use these as a model for human mammary gland development as it relates to human breast cancer risks. To begin this process, we conducted a pilot study, comparing gene expression profiles of lactating bovine mammary tissue against nonlactating tissue on the BMAM microarray. Our results have yielded many novel and interesting genes exhibiting differential expression in lactating mammary tissue, including oncogenes (VAV3, C-myc), mediators of apoptosis (Caspase 8), and cell cycle regulators (LASP1).

Gene expression profiling of the bovine gastrointestinal tract

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 639-649 ◽  
Author(s):  
Christiane Hansen ◽  
Anna Fu ◽  
Yan Meng ◽  
Erasmus Okine ◽  
Rachel Hawken ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gastrointestinal Tract ◽  
Expressed Sequence Tags ◽  
Expression Profiling ◽  
Cdna Libraries ◽  
Gi Tract ◽  
Consensus Sequences ◽  
Similarities And Differences ◽  
Expressed Sequence ◽  
Gene Expression Levels

Basal gene expression levels across the bovine gastrointestinal tract (GI) were examined in an attempt to formulate genetic explanations for the differences in function that are known or thought to exist between the various regions. Gene expression along the tract was studied through the random sequencing of a total of 16 412 clones from seven tissue-specific cDNA libraries spanning its length. The expressed sequence tags (ESTs) within each library were clustered to reduce clone redundancy and obtain longer consensus sequences. BLASTN and BLASTX searches against the NCBI human RefSeq databases were used to find putative matches for the bovine sequences and gene ontology assignments were made. Notable similarities and differences in gene expression were observed among the various compartments of the GI tract of the bovine. Many of the prominent transcripts have yet to be reliably identified and the prominence of others may be worthy of further examination. This collection of ESTs represents an important resource for the future construction of a GI tract specific microarray for further gene expression studies.Key words: gene expression, EST, gastrointestinal tract, cattle.

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