Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23605400_1.fastq.gz | Fastqsanger.gz | |||
| SRR23605400_2.fastq.gz | Fastqsanger.gz | |||
| SRR23605401_1.fastq.gz | Fastqsanger.gz | |||
| SRR23605401_2.fastq.gz | Fastqsanger.gz | |||
| SRR23605402_1.fastq.gz | Fastqsanger.gz |
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Project description:Four small RNA libraries from two contrasting sweet sorghum genotypes were sequenced. In this study, One hundred and ninety-five conserved miRNAs belonging to 56 families and 25 putative novel miRNAs from 28 precursors were identified, among which 38 conserved and 24 novel miRNAs were differentially expressed under Cd stress and/or between H18 and L69. Two groups of them: miR169p/q-nov_23 and miR408 were further focused through the coexpression analysis and might be involved in Cd transport, cytoskeleton activity and cell wall construction by regulating their targets. This study presents new insights into the regulatory roles of miRNAs in Cd accumulation and tolerance in sweet sorghum and will help to develop high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum through molecular breeding and/or genetic engineering approaches.
2023-10-12 | GSE145617 | GEO
Project description:Common SNPs for GBS data for global sorghum germplasm incluiding Sorghum association pannel, carotenoid panel, Haiti breeding program, NPGS collection for Sudan and Ethiopia, Niger germplasm and Nigeria germplasm
2023-03-06 | PRJEB60406 | EVA
Project description:Sorghum (Sorghum bicolor L. Moench) is a C4 species sensitive to the cold spring conditions that occur at northern latitudes, usually coupled with excessive light, and that greatly affects the photosynthetic rate. The objective of this study was to discover genes/genomic regions that control the capacity to cope with excessive energy under low temperature conditions during the vegetative growth period. A genome-wide association study (GWAS) was conducted for eight photosynthesis and chlorophyll fluorescence traits under three consecutive temperature treatments: control (28°C/24°C), cold (15°C/15°C) and recovery (28°C/24°C). Cold stress significantly reduced the photosynthetic capacity of sorghum plants and a total of 204 genomic regions were discovered associated with at least one trait in a particular treatment or in the time integrated response to cold. If no GBS markers were available for the targeted candidate genes, new SNPs were developed and genotyped using a SNPtype™ Assay (Fluidigm) on the Fluidigm BioMarkHD system and GT 96.96 Dynamic Array Integrated Fluidic Circuits of Fluidigm.
2017-08-10 | GSE102452 | GEO
Project description:In the present study, genomic binding sites of glucocorticoid receptors (GR) were identified in vivo in the rat hippocampus applying chromatin immunoprecipitation followed by next-generation sequencing. We identified 2470 significant GR-binding sites (GBS) and were able to confirm GR binding to a random selection of these GBS covering a wide range of P values. Analysis of the genomic distribution of the significant GBS revealed a high prevalence of intragenic GBS. Gene ontology clusters involved in neuronal plasticity and other essential neuronal processes were overrepresented among the genes harboring a GBS or located in the vicinity of a GBS. Male adrenalectomized rats were challenged with increasing doses of the GR agonist corticosterone (CORT) ranging from 3 to 3000 μg/kg, resulting in clear differences in the GR-binding profile to individual GBS. Two groups of GBS could be distinguished: a low-CORT group that displayed GR binding across the full range of CORT concentrations, and a second high-CORT group that displayed significant GR binding only after administering the highest concentration of CORT. All validated GBS, in both the low-CORT and high-CORT groups, displayed mineralocorticoid receptor binding, which remained relatively constant from 30 μg/kg CORT upward. Motif analysis revealed that almost all GBS contained a glucocorticoid response element resembling the consensus motif in literature. In addition, motifs corresponding with new potential GR-interacting proteins were identified, such as zinc finger and BTB domain containing 3 (Zbtb3) and CUP (CG11181 gene product from transcript CG11181-RB), which may be involved in GR-dependent transactivation and transrepression, respectively. In conclusion, our results highlight the existence of 2 populations of GBS in the rat hippocampal genome. - See more at: http://press.endocrine.org/doi/10.1210/en.2012-2187?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed#sthash.LqK088DP.dpuf
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Project description:Transcriptional profiling of cotton fiber cells from two cotton germplasm lines, MD 52ne and MD 90ne. Comparison of fiber cell transcription profiles is between the two germplasm lines and over a developmental time-course from 8 to 24 days post anthesis in four day intervals. Cotton plants grown in 3-4 row plots of approximately 300-400 individual plants. Bulked fiber samples from multiple plants per each plot represented a biological replication. There were 3-4 spatially distinct plots per cotton germplasm line. Loop microarray hybridization experimental design. Biological replicates: 2 for each germplasm line at each time-point. Technical replicates: 2 for each germplasm line at each time-point (dye-swap).
2010-05-07 | E-GEOD-14388 | biostudies-arrayexpress
Project description:The CiaRH and LiaFSR two-component regulatory systems in Streptococcus agalactiae (Group B Streptococcus, GBS) are essential mediators of the organism s response to biologically important sources of environmental stress, and positive regulators of GBS virulence. Transcriptional profiling of CiaR mutant GBS and LiaR mutant GBS reveals that LiaR is positively-regulated by CiaR, and the individual mutant transcriptomes share a number of commonly-regulated genes. To determine the GBS response to loss of both of these key regulatory systems, we constructed a GBS mutant strain with non-polar deletions in both ciaR and liaR, and performed transcriptional profiling using DNA microarray analysis, comparing wild-type GBS to CiaR/LiaR double mutant GBS under non-stressed conditions.
2012-11-18 | GSE14572 | GEO
Project description:Group B Streptococcus (GBS) is a pervasive perinatal pathogen, yet factors driving GBS dissemination in utero are poorly defined. Gestational diabetes mellitus (GDM), a complication marked by dysregulated immunity and maternal microbial dysbiosis, increases risk for GBS perinatal disease. We interrogated host-pathogen dynamics in a novel murine GDM model of GBS colonization and perinatal transmission. GDM mice had greater GBS in utero dissemination and subsequently worse neonatal outcomes. Dual-RNA sequencing revealed differential GBS adaptation to the GDM reproductive tract, including a putative glycosyltransferase (yfhO), and altered host responses. GDM disruption of immunity included reduced uterine natural killer cell activation, impaired recruitment to placentae, and altered vaginal cytokines. Lastly, we observed distinct vaginal microbial taxa associated with GDM status and GBS invasive disease status. Our translational model of GBS perinatal transmission in GDM hosts recapitulates several clinical aspects and enables discovery of host and bacterial drivers of GBS perinatal disease.
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Project description:Sorghum is multipurpose crop worldwide serving as food, feed, and feedstock for biofuels, whose floral transition and vegetative growth heavily depend on photoperiod. Although multiple sorghum maturity loci (Ma1-Ma6) have been associated with photoperiod sensitivity in previous QTL studies, the underlying molecular mechanisms remain poorly understood. By functional characterizing sorghum SbGhd7 (Ma6) and integrating RNA-seq analysis of Ghd7 overexpression sorghum, ChIP-seq analysis of SbGhd7 binding sites in protoplasts and molecular studies, we discovered that SbEhd1 and SbFT10 are the direct targets of SbGhd7. SbGhd7 is a transcriptional repressor and inhibits florigen-induced floral transition by repressing SbEhd1 and SbFT10 expression.
2024-01-30 | GSE238094 | GEO