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In silico comparative transcriptome analysis of Papaver somniferum cultivars

100%

Tan T. G., Turktas M., Guclu G.

Acta Scientiarum Polonorum. Hortorum Cultus

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2023

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tom 22

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nr 6

2

Transcriptomic and physiological insights into sprout regeneration of cinnamomum camphora under logging wound management

100%

Xiaoxing Z., Yi L., Gao B., Gao Y., Wu X., Huang S., Pan Y., Dong L., Zou S.

Acta Agrobotanica

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2026

|

tom 79

3

Molecular identification, transcriptome sequencing and functional annotation of Pulex irritans

75%

Hu L., Zhao Y., Yang Y., Zhang W., Guo H., Niu D.

Acta Parasitologica

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2021

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tom 66

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nr 2

4

Integrating expression data and genomic sequences to investigate transcriptional regulation in barley in response to abiotic stress

75%

Delavari A., Zinati Z., Sazegari S., Tahmasebi A.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2021

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tom 102

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nr 1

5

Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses

75%

Jazayeri S. M., Pooralinaghi M., Torres-Navarrete Y., Oviedo-Bayas B., Guerra I. E., Jacome D. H., Moran C. Q., Macias C. S., Escobar K. M., Ghafoor S. M. H. A. S., Veiskarami G., Jandaghi P., Torres R. O. V.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2022

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tom 103

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nr 4

6

Transcriptome analysis of enzyme activities regulating ROS metabolism in olive (Olea europaea L.) reproductive tissues

63%

Zafra A., Carmona R., Jimenez-Quesada M., Traverso J., Castro A., Rodriguez-Garcia M., Bautista R., Claros M., Alche J.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

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nr 2

7

Isolation of biosynthesis related transcripts of 2,3,5,4'-tetrahydroxy stilbene-2-O-beta-D-glucoside from Fallopia multiflora by suppression subtractive hybridization

63%

Zhao W., Sheng S., Liu Z., Lu D., Zhu K., Li X., Zhao S., Yao Y.

Acta Societatis Botanicorum Poloniae

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2014

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tom 83

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nr 2

2,3,5,4'-tetrahydroxy stilbene-2-O-ß-D-glucoside (THSG) exerts multiple pharmacodynamic actions, found in Fallopia multiflora, but the biosynthesis pathway of THSG is still unclear. To clear this ambiguity, we constructed suppression subtractive hybridization (SSH) libraries to screen the genes involved in THSG biosynthesis from two F. multiflora varieties, which vary significantly in THSG content. Twelve non-redundant differentially expressed sequence tags were obtained and the full lengths of 4 unreported fragments were amplified by rapid amplification of cDNA ends. We totally got 7 fulllength transcripts, and all of them were aligned to the transcriptome and digital gene expression tag profiling database of four F. multiflora tissues (root, stem and leaf from Deqing F. multiflora and another root from Chongqing F. multiflora; data unpublished) using local BLAST. The results showed that there was a significant, organ specific difference in the expression of fragments and full-length sequences. All the sequences were annotated by aligning to nucleotide and protein databases. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that THSG biosynthesis was correlated with multiple life activities.

8

ROSMETER: a bioinformatic tool for the identification of reactive oxygen species (ROS) transcriptomic imprints

63%

Rosenwasser S., Sela N., Fluhr R., Friedman H.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

|

tom 94

|

nr 2

9

Consequences of mitochondrial translation perturbation for the whole cell transcriptome

63%

Adamowicz A., Kwasniak M., Janska H.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

|

tom 94

|

nr 3

10

Transcriptome and proteome changes accompanying increased vigor of osmoprimed rape (Brassica napus L.) seeds

63%

Kubala S., Lechowska K., Wojtyla L., Kosmala A., Quinet M., Lutts S., Garnczarska M.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

|

tom 94

|

nr 3

11

RNA-seq reveals differentially expressed genes in cucumber MSC lines possessing mitochondrial DNA rearrangements

63%

Mroz T., Pryszcz L., Skarzynska A., Kielkowska A., Havey M., Bartoszewski G.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

|

tom 94

|

nr 2

12

De novo sequencing and comparative transcriptome analysis of white petals and red labella in Phalaenopsis for discovery of genes related to flower color and floral differentiation

63%

Yang Y., Wang J., Ma Z., Sun G., Zhang C.

Acta Societatis Botanicorum Poloniae

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2014

|

tom 83

|

nr 3

Phalaenopsis is one of the world’s most popular and important epiphytic monopodial orchids. The extraordinary floral diversity of Phalaenopsis is a reflection of its evolutionary success. As a consequence of this diversity, and of the complexity of flower color development in Phalaenopsis, this species is a valuable research material for developmental biology studies. Nevertheless, research on the molecular mechanisms underlying flower color and floral organ formation in Phalaenopsis is still in the early phases. In this study, we generated large amounts of data from Phalaenopsis flowers by combining Illumina sequencing with differentially expressed gene (DEG) analysis. We obtained 37 723 and 34 020 unigenes from petals and labella, respectively. A total of 2736 DEGs were identified, and the functions of many DEGs were annotated by BLAST-searching against several public databases. We mapped 837 up-regulated DEGs (432 from petals and 405 from labella) to 102 Kyoto Encyclopedia of Genes and Genomes pathways. Almost all pathways were represented in both petals (102 pathways) and labella (99 pathways). DEGs involved in energy metabolism were significantly differentially distributed between labella and petals, and various DEGs related to flower color and floral differentiation were found in the two organs. Interestingly, we also identified genes encoding several key enzymes involved in carotenoid synthesis. These genes were differentially expressed between petals and labella, suggesting that carotenoids may influence Phalaenopsis flower color. We thus conclude that a combination of anthocyanins and/or carotenoids determine flower color formation in Phalaenopsis. These results broaden our understanding of the mechanisms controlling flower color and floral organ differentiation in Phalaenopsis and other orchids.

13

Transcriptome signature of the lactation process, identified by meta-analysis of microarray and RNA-Seq data

63%

Farhadian M., Rafat S. A., Hasanpur K., Ebrahimie E.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2018

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tom 99

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nr 2

14

Transcriptomic 'portraits' of canine mammary cancer cell lines with various phenotypes

63%

Krol M., Pawlowski K. M., Skierski J., Turowski P., Majewska A., Polanska J., Ugorski M., Morty R. E., Motyl T.

Journal of Applied Genetics

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2010

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tom 51

|

nr 2

169-183

In light of the high incidence of mammary cancer in dogs and completion of the canine genome sequencing, the new possibilities of gene profiling by using DNA microarrays give hope to veterinary oncology. The cell lines isolated from mammary tumors are a valuable tool in developing and testing new pathway-specific cancer therapeutics. Differential cytometric analysis of 6 canine mammary cancer cell lines was performed. We divided cell lines into 3 groups based on their phenotype: 2 lines with high proliferative potential, 2 lines with high antiapoptotic potential, and 2 lines with high metastatic potential. DNA microarray analysis revealed common genes for cell lines of each group. We found that genes encoding the receptors for growth hormone and ghrelin are related to high proliferation rate, while ABR (active BCR-related) and TMD1 (TM2 domain containing 1) genes are related to a high antiapoptotic potential of the cancer cells. Metastatic properties of mammary cancer cells seem to be associated with elevated expression of PGP (P glycoprotein), SEMA3B (semaphorin 3B), and STIM1 (stromal interaction molecule 1).

15

Anti-inflammatory effects of atorvastatin treatment in chronic obstructive pulmonary disease. A controlled pilot study

63%

Mroz R. M., Lisowski P., Tycinska A., Bierla J., Trzeciak P. Z., Minarowski L., Milewski R., Lisowska A., Boros P., Sobkowiak B., Duszewska A. M., Chyczewska E., Musial W. J., Macnee W.

Journal of Physiology and Pharmacology

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2015

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tom 66

|

nr 1

16

Differential transcriptomic analysis by RNA-seq of GSNO-responsive genes between Arabidopsis roots and leaves

51%

Begara-Morales J., Sanchez-Calvo B., Luque F., Laterrier M., Valderrama R., Mata-Perez C., Padilla M., Carreras A., Corpas F., Barroso J.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

|

tom 94

|

nr 2

17

Functional genome research in reproductive biology and biotechnology - a minireview

51%

Wolf E., Bauersachs S.

Animal Science Papers and Reports

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2010

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tom 28

|

nr 2

Female infertility is an increasingly important problem in cattle, causing enormous costs and retarding genetic progress. Current attempts to improve fertility by genetic selection are inefficient due to the low heritability of the respective trait, i.e. the nonreturn-rate 90 days after first sernice (NRR 90). Thus novel phenotypic traits more closely related to fertility are urgently needed.Since a large proportion of pregnancy losses occur in the preimplantation period, the interaction between early embryos and their maternal environment is an attractive target for systematic investigations, which may uncover mechanisms underlying early embryonic death. Based on holistic transcriptome and proteome studies [Hiendleder et al. 2005, Wolf et al. 2006] we attempt to understand the quantitative biology of embryo maternal communication and the regulation of endometrial receptivity [Wolf et al. 2003]. A short-term goal is the development of array-based systems for the differential diagnosis of fertility problems and for evaluating the connection between metabolic disturbances and reproductive functions. A long-term goal is the identification of genetic variation affecting the fertility-related gene expression profiles in female reproductive tissues such as endometrium. The endometrium undergoes marked functional changes during estrous cycle and pregnancy. As the adjacent environment of the conceptus, it represents the maternal interface for embryo maternal communication, which is essential to maintain pregnancy. Transcriptome studiem provide the unique opportunity to assess molecular profiles changing in response to endocrine or metabolic stimuli or to embryonic pregnancy recognition signals [reviewed in Bauersachs et al. 2008, Spencer et al. 2008].

18

Transcriptome sequencing: next generation approach to RNA functional analysis

51%

Zmienko A., Jackowiak P., Figlerowicz M.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2011

|

tom 92

|

nr 4

19

Age-dependent changes in bovine skeletal muscle transcriptomic profile

51%

Sadkowski T., Jank M., Oprzadek J., Motyl T.

Journal of Physiology and Pharmacology. Supplement

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2006

|

tom 57

|

nr 7

95-110

The postnatal growth of muscle tissue occurs by hypertrophy comprising satellite cells proliferation, differentiation and protein turnover. The highest rate of skeletal muscle gains and protein synthesis in bulls occurs in the period between 180 and 360 days of postnatal life. However, genes which are responsible for quantitative and qualitative changes in skeletal muscle during this period are not identified up to date. The aim of our study was to compare the changes in transcriptomic profile of skeletal muscle (m. semitendinosus) in 12 Polish Black and White bulls between 6 and 12 month of life. For experimental purposes we used bovine cDNA microarray (the NBFGC EST collection) which contains 18,263 unique genes, derived from many different tissue types and various physiologically important states within these tissues. Our results revealed 53 genes which expression changed in the same manner depending on age of all examined pairs of animals. Thirty two of these genes showed at least 2-fold difference in expression between two analyzed age points. Age-dependent up-regulation was the most pronounced in the case of following genes: similar to MAD2L1 binding protein, similar to thymocyte potein thy28 isoform 1, similar to type I inositol-1,4,5-triphosphate 5-phosphatase, similar to nucleoside diphosphate kinase 6, proline rich 14, similar to transcription factor E2-alpha and phospholipase C gamma 1. The highest age-dependent decrease of the transcript was observed in the case of: similar to ubiquitin carboxy-terminal hydrolase L1, similar to latent TGF-beta binding protein 3 precursor, phospho-mannomutase 2, CD74 antigen, simlar to BCL6 co-represor-like 1, plateled/endothelial cell adhesion molecule (PECAM1), necdin, zygin, tight junction protein 3, ankyrin and apolipoprotein-L3. Although the role of the most of above genes and interactions between products of their expression is not clear at the moment, the significance of their response between 6 and 12 month of age may indicate their involvement in growth, development and metabolic changes in bovine skeletal muscle during the first year of postnatal life.

20

Pre- and postnatal differential gene expression with relevance for meat and carcass traits in pigs - a review

51%

Wimmers K., Murani E., Ponsuksili S.

Animal Science Papers and Reports

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2010

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tom 28

|

nr 2

Pre- and postnatal processes determine the final outcome of breeding of pigs in terms of traits related to carcass and meat quality at slaughter. In particular, the number of myofibers and to a large extent their metabolic and contractile properties, which also influence their size, are determined prenatally during the process of myogenesis. By this, postnatal muscle growth and parameters of meat quality are modulated. The metabolic balance, biochemical and biophysical preslaughter properties of muscle prior to slaughter determine the process of maturation of muscle to meat.Thus, differential regulation of the abundance of transcripts of biological networks in prenatal and postnatal muscle affect biochemical processes of meat maturation. In general, because the traits of interest are typically not expressed at prenatal stages, no direct relationship between phenotype and gene expression pattern can be established. However, trait-related differential expression within any prenatal developmental stage can be assessed based on known estimated breeding values, known QTL-genotypes and/or based on breed differences. Expression profiles of muscle at slaughter can directly be linked to meat quality. A suitable experimental design of “matched samples” is the discordant sib pair design. Here it is exemplarily discussed that differentially expressed transcript profiles of M. longissimus dorsi at prenatal and postnatal stages offer an insight into the biological processes in the live muscle that affect the process of meat maturation and finally meat quality.

Ograniczanie wyników

In silico comparative transcriptome analysis of Papaver somniferum cultivars

Transcriptomic and physiological insights into sprout regeneration of cinnamomum camphora under logging wound management

Molecular identification, transcriptome sequencing and functional annotation of Pulex irritans

Integrating expression data and genomic sequences to investigate transcriptional regulation in barley in response to abiotic stress

Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses

Transcriptome analysis of enzyme activities regulating ROS metabolism in olive (Olea europaea L.) reproductive tissues

Isolation of biosynthesis related transcripts of 2,3,5,4'-tetrahydroxy stilbene-2-O-beta-D-glucoside from Fallopia multiflora by suppression subtractive hybridization

ROSMETER: a bioinformatic tool for the identification of reactive oxygen species (ROS) transcriptomic imprints

Consequences of mitochondrial translation perturbation for the whole cell transcriptome

Transcriptome and proteome changes accompanying increased vigor of osmoprimed rape (Brassica napus L.) seeds

RNA-seq reveals differentially expressed genes in cucumber MSC lines possessing mitochondrial DNA rearrangements

De novo sequencing and comparative transcriptome analysis of white petals and red labella in Phalaenopsis for discovery of genes related to flower color and floral differentiation

Transcriptome signature of the lactation process, identified by meta-analysis of microarray and RNA-Seq data

Transcriptomic 'portraits' of canine mammary cancer cell lines with various phenotypes

Anti-inflammatory effects of atorvastatin treatment in chronic obstructive pulmonary disease. A controlled pilot study

Differential transcriptomic analysis by RNA-seq of GSNO-responsive genes between Arabidopsis roots and leaves

Functional genome research in reproductive biology and biotechnology - a minireview

Transcriptome sequencing: next generation approach to RNA functional analysis

Age-dependent changes in bovine skeletal muscle transcriptomic profile

Pre- and postnatal differential gene expression with relevance for meat and carcass traits in pigs - a review