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Protocols

CottonGen specifications

Information


Unique identifier OMICS_04488
Name CottonGen
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Dorrie Main

Additional information


https://www.cottongen.org/userManual

Publication for CottonGen

CottonGen citations

 (37)
library_books

Evolution and Stress Responses of Gossypium hirsutum SWEET Genes

2018
Int J Mol Sci
PMCID: 5877630
PMID: 29517986
DOI: 10.3390/ijms19030769

[…] ilable online: http://gsds.cbi.pku.edu.cn/) []. Meanwhile, the physical positions of all cotton SWEET genes on chromosomes were determined according to the genome annotation files downloaded from the CottonGen website (available online: https://www.cottongen.org). The SWEET genes were mapped using MapInspect software [] or Circos (version 0.69) software []. Tandem duplications were analyzed on the […]

library_books

Inhibition of Heat Shock proteins HSP90 and HSP70 induce oxidative stress, suppressing cotton fiber development

2018
Sci Rep
PMCID: 5827756
PMID: 29483524
DOI: 10.1038/s41598-018-21866-0

[…] HSP90 and HSP70 protein sequences were used as a query to perform BlastP similarity search (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) against G. hirsutum proteome data available at CottonGen database. The sequences obtained were analyzed for the presence of characteristic domains of both the families using Conserved Domain Database (CDD; https://www.ncbi.nlm.nih.gov/Structure/cd […]

library_books

Identification of Gossypium hirsutum long non coding RNAs (lncRNAs) under salt stress

2018
BMC Plant Biol
PMCID: 5785843
PMID: 29370759
DOI: 10.1186/s12870-018-1238-0

[…] low-quality reads and trimming the reads whose number of N bases accounted for more than 5% (quality score, Q ≥ 30). The reference G. hirsutum genome and the annotation files were downloaded from the CottonGen database (http://www.cottongen.org). We built the genome index using Bowtie2 v2.2.3 [], and clean data was mapped to the G. hirsutum genome using TopHat v2.0.12 []. TopHat calls Bowtie2 for […]

call_split

Gbvdr6, a Gene Encoding a Receptor Like Protein of Cotton (Gossypium barbadense), Confers Resistance to Verticillium Wilt in Arabidopsis and Upland Cotton

2018
Front Plant Sci
PMCID: 5776133
PMID: 29387078
DOI: 10.3389/fpls.2017.02272
call_split See protocol

[…] pro/scan.html), and SMART (http://smart.embl-heidelberg.de/). The sequences of the SSR markers that flank Verticillium wilt-resistance quantitative trait loci (QTL) in cotton were downloaded from the CottonGen (https://www.cottongen.org) and CottonQTLdb (http://www2.cottonqtldb.org:8081/search) websites. The physical locations of genes and markers were determined by anchoring their sequences onto […]

call_split

QTL Mapping for Fiber Quality and Yield Traits Based on Introgression Lines Derived from Gossypium hirsutum × G. tomentosum

2018
Int J Mol Sci
PMCID: 5796191
PMID: 29342893
DOI: 10.3390/ijms19010243
call_split See protocol

[…] reads (quality score ˂ 20 e) were first filtered out. Then, each of the high-quality reads was trimmed off by 5 bp at the terminal site []. The reference genome TM-1 sequence was downloaded from the CottonGen database (https://www.cottongen.org). Clean reads from each sample were achieved and mapped to the G. hirsutum TM-1 genome [] using Burrows-Wheeler-Aligner (BWA, v0.7.10) software []. The ma […]

library_books

Structural, expression and evolutionary analysis of the non specific phospholipase C gene family in Gossypium hirsutum

2017
BMC Genomics
PMCID: 5738194
PMID: 29258435
DOI: 10.1186/s12864-017-4370-6

[…] rg.cn/page/species/index.jsp#, Gossypium_hirsutum_v1.0), respectively. The G. arboretum genome (G.arboreum_BGI-A2_v1.0) and the G. raimondii genome (G.raimondii_JGI_221_v2.1) were downloaded from the CottonGen (https://www.cottongen.org/). Then, local databases were constructed. Arabidopsis NPC sequences obtained from The Arabidopsis Information Resource (TAIR, http://www.arabidopsis.org/) were us […]

Citations

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CottonGen institution(s)
Department of Horticulture, Washington State University, Pullman, WA, USA; Cotton Incorporated, Cary, NC, USA; Crop Germplasm Research Unit, USDA-ARS-SPARC, College Station, TX, USA
CottonGen funding source(s)
Supported by Cotton Incorporated; the USDA-ARS Crop Germplasm Research Unit at College Station, TX; Southern Association of Agricultural Experiment Station Directors; Bayer CropScience; Dow/Phytogen; Monsanto.

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