GEO DataSets

(Submitter supplied) Xanthomonas spp. employ transcription activator-like effectors (TALEs) to promote pathogenicity by activating host susceptibility (S) genes. Cotton GhSWEET10 is an S gene targeted by a TALE in an early isolate of Xanthomonas citri pv. malvacearum (Xcm), but not by recent field Xcm isolates. To understand the pathogenicity shift in Xcm and its adaptation to cotton, we assembled the whole genome and the TALE repertoire of three recent Xcm Texas field isolates. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

6 Samples

Download data: XLSX

(Submitter supplied) Salinity is a major abiotic stress at critical stages of seed germination and seedling establishment. Germination rate (GR) and field emergence rate (FER) are the key traits that determine the basic number of plants stand under field conditions. To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines (RILs) and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, Number of main stem leaves) in 2016-2018. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

27 Samples

Download data: XLSX

(Submitter supplied) We compared different days post-anthesis (5DPA, 10DPA, 15DPA and 25DPA) differentially expressed genes (DEGs) in fiber development between G. hirsutum and G. barbadense. In addition, we analysis the differentially expressed genes (DEGs) function using the database for annotation, visualization and integrated discovery (DAVID). Overall, gene expression pattern have significantly difference between G. more...

Organism:

Gossypium barbadense; Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16485 GPL19651

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

54 Samples

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(Submitter supplied) Patterns of indeterminate and determinate growth specify plant architecture and influence crop productivity. In cotton (Gossypium hirsutum), SINGLE FLOWER TRUSS (SFT) stimulates the transition to flowering and determinate growth while its closely related antagonist SELF-PRUNING (SP) maintains meristems in indeterminate states to favor vegetative growth. To identify the molecular programs regulating cotton growth habits, and understand how altered expression of GhSFT and GhSP perturbs these programs, we used RNA-Seq to determine the gene expression networks involved in wild photoperiodic, domesticated day-neutral, and GhSFT- and GhSP-regulated architectures. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

18 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Each plant's architecture, composed of patterns of indeterminate and determinate growth, is defined through the activities of meristems. Understanding the regulation of meristem identity can benefit plant architecture and crop yield. To understand how meristem activities contribute to different architectures in cotton (Gossypium hirsutum), we used RNA-Seq to determine the transcriptomes from meristems isolated from different developmental stages of wild photoperiodic and domesticated day-neutral cotton grown under different photoperiods.

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

36 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Purpose: found out the regulated genes of nulliplex-branch and its forming molecular mechanism Methods: the GhBRC1 genes of nulliplex branch and short branch cotton are silenced by VIGS, and then the shoot apical mRNA of controls and treated were sequenced, in four repeats, using Illumina HiSeq 2000. Results: we found 3519 and 17 differnent expressed genes in nulliplex-branch and short branch cotton, respectively. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

16 Samples

Download data: TXT

(Submitter supplied) Compare the expression profiles of natural brown and green cotton fibers, and white color fiber at 0 and 12 days post-anthesis (DPA) to identify genes involved in pigment synthesis

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

12 Samples

Download data: XLS

(Submitter supplied) Purpose:Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology. And quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods:We investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16485

12 Samples

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(Submitter supplied) Background: Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties. In an effort to uncover the transcripts and miRNA networks involved in plant height, the transcriptome and small RNA sequencing were performed based on dwarf mutant Ari1327 (A1), tall-culm mutant Ari3697 (A3) and wild type Ari971 (A9) in Gossypium hirsutum. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16485

6 Samples

Download data: FA, TXT

(Submitter supplied) High temperature (HT) stress is a major environmental stress that limits cotton growth, metabolism, and yield worldwide. The identification and characterization of thermotolerance is restricted by the plant growth environment and growth stage. In this study, four genotypes of upland cotton (Gossypium hirsutum L.) with known field thermotolerance were evaluated under normal and HTs at the seedlings stage in a growth cabinet with 11 physiological, biochemical, and phenotypic assays. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

6 Samples

Download data: FA, TXT

(Submitter supplied) To gain insight into the functions of salt-regulated miRNAs, target genes were identified through degradome sequencing approach. Three cotton RNA libraries were constructed and sequenced under normal consideration, osmotic and ionic stress. A total of 73,988,644 reads represented by 3,254,054 unique reads from the 5’ ends of uncapped and poly-adenylated RNAs were obtained. The PairFinder software was used to identify the sliced targets for the known miRNAs and novel miRNAs. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

3 Samples

Download data: TXT

(Submitter supplied) Plants respond to stress by using multiple gene regulatory mechanisms including the post-transcriptional regulation of gene expression. The stresses suffered by plants under salinity include osmotic stress and ion stress. In this study, three cotton small RNA libraries were constructed and sequenced under normal consideration, osmotic and ionic stress. The length distribution of obtained small RNAs was significantly different between libraries. more...

Organism:

Gossypium hirsutum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16485

3 Samples

Download data: TXT

(Submitter supplied) Purpose: found out the regulated genes of nulliplex-branch and its forming molecular mechanism Methods: shoot apical mRNA and miRNA in two nulliplex branch and two normal branch cotton of three development stages were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Results: we found 3 825 and 353 specific stage differnent expressed genes in pre-budding stage of island cotton and upland cotton, respectively. more...

Organism:

Gossypium barbadense; Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL16485 GPL19651

72 Samples

Download data: TXT

(Submitter supplied) Nitric oxide(NO) is emerging as an important signaling molecule with diverse physiological functions in plants, leading to a necessity to discover the downstream genes and signal transduction network modulated by NO. In the current study, changes in gene expression in response to NO were studied in upland cotton(Gossypium hirsutum) using Solexa/Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing method. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

5 Samples

Download data: TXT

(Submitter supplied) Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter. Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. more...

Organism:

Gossypium barbadense; Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16485 GPL19651

30 Samples

Download data: FA, XLSX

(Submitter supplied) We used a next-generation sequencing approach, Illumina Digital Gene Expression II (DGEII) technology, to Genome-wide profiling of gene expression during somatic (SE) and zygotic embryo (ZE) development. As a result, 4242 differentially expressed genes (DEGs) were identified between SE and ZE. Expression pattern cluster and functional classification analysis of the differentially expressed genes revealed that large number of genes indicative of response to stress highly expressed in somatic embryos. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Gossypium hirsutum

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL16485 GPL9362

7 Samples

Download data: TXT

(Submitter supplied) In this study, in order to identify miRNA targets, a degradome library derived from anthers of the WT and GMS (Genetic Male Sterility) mutant representing three stages of development was constructed and sequenced, resulting in the generation of 24.6 million raw reads. After removal of low quality sequences and adapter sequences, 24.4 million clean reads were obtained and 98% were 20 or 21 nt in length as expected in that normally length distribution peak of degradome fragment is between 20 and 21 nt [Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ: Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. more...

Organism:

Gossypium hirsutum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16485

1 Sample

Download data: TXT