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Protocols

dbEST specifications

Information


Unique identifier OMICS_06109
Name dbEST
Alternative name Database of Expressed Sequence Tags
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Todd M. Lowe
  • person_outline Mark Boguski

Additional information


https://www.ncbi.nlm.nih.gov/dbEST/

Publication for Database of Expressed Sequence Tags

dbEST citations

 (342)
call_split

18FDG PET/CT and molecular markers to predict response to neoadjuvant chemotherapy and outcome in HER2 negative advanced luminal breast cancers patients

2018
Oncotarget
PMCID: 5893244
PMID: 29662649
DOI: 10.18632/oncotarget.24674
call_split See protocol

[…] with Taqman probes (Eurogentec, Liège, Belgium). Primers and fluorescent probes were designed from published sequences using Primer express software (Applied Biosystems Inc.). BLASTN searches against dbEST and nr (the non-redundant set of the GenBank sequence database) were performed to confirm the total gene specificity of the chosen nucleotide sequences and the absence of DNA polymorphisms. Prim […]

library_books

Notos a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types

2018
BMC Bioinformatics
PMCID: 5870242
PMID: 29587630
DOI: 10.1186/s12859-018-2115-4

[…] We investigated the performance of the Silverman test, the different criteria, and Notos on our data base with 603 species from dbEST. Table  shows the results from 17 arbitrarily chosen species, which display patterns that are representative of the full sample. The principal results are the following: (i)The test of Silverma […]

call_split

Electronic Northern Analysis of Genes and Modeling of Gene Networks Underlying Bovine Milk Fat Production

2017
PMCID: 5698600
PMID: 29250447
DOI: 10.1155/2017/1910530
call_split See protocol

[…] The reference bovine gene sequences for 45 genes, previously known to be involved in lipid synthesis () [], were obtained from Ensembl []. Electronic Northern (e-Northern) was performed using dbEST and UniGene; briefly, the dbEST [] was queried for these sequences by BLASTN v2.2.27 [] using default parameters and the significant hits were looked up in UniGene ESTProfile [] for transcript a […]

library_books

High PTPN13 expression in high grade serous ovarian carcinoma is associated with a better patient outcome

2017
Oncotarget
PMCID: 5707051
PMID: 29221157
DOI: 10.18632/oncotarget.21175

[…] oduct size 80bp, annealing temperature 61°C; median CTs = 27.85; PCR efficiency >98%).The specificity of the chosen primer sequences was confirmed by using the BLASTN nucleotide-nucleotide tool and a database of expressed sequence tags and nr (the non-redundant set of the GenBank, EMBL and DDBJ database sequences). To check for amplification of contaminating genomic DNA, one of the two primers con […]

library_books

GBF3 transcription factor imparts drought tolerance in Arabidopsis thaliana

2017
Sci Rep
PMCID: 5567290
PMID: 28831141
DOI: 10.1038/s41598-017-09542-1

[…] 0% field capacity (FC), 60% FC and 35% FC was used as drought sample and 100% FC as control. From the library, 156 clones were sequenced and annotated using NCBI BLASTX database and submitted to NCBI dbEST database. Among the sequenced clones, there were 139 unique expressed sequence tags (ESTs) (Supplementary Table ). Based on the putative functions ESTs were classified into four broad functional […]

library_books

Identification of Endogenous Reference Genes for RT qPCR Expression Analysis in Urochloa brizantha Under Abiotic Stresses

2017
Sci Rep
PMCID: 5561021
PMID: 28819216
DOI: 10.1038/s41598-017-09156-7

[…] AF), FTSH protease 4 (FTSH), Succinyl-coa ligase (SucCoa), Tubulin alfa-5 (α-TUB5) and Ubiquitin conjugating enzyme (UbiCo). The accession numbers were used to search for nucleotide sequences against dbest database in the GenBank, which in turn, were used to design the primers. To search for ESTss of Actin 12 (ACT12) and Tubulin beta-6 (β-TUB6) genes of U. brizantha, sequences of switchgrass (Pani […]

Citations

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dbEST institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

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