RNA-seq analysis of gene expression after exposure to hot and cold stress in WT cells of Thermosynechococcus elongatus, BP-1
ABSTRACT: To investigate the temperature response in Thermosynechococcus elongatus (BP-1) and look for coordinated control in the cell, transcriptomes of BP-1 were measured using RNAseq following exposure to low and high temperature stress. The amount of temperature increase (53 to 61 °C) and decrease (53 to 45 °C) was based on the allowable range of continuous growth. The cells were growth in three separate culture tubes under LED light in a temperature-controlled submersible chamber under batch growth conditions. The temperature shift was conducted once the cells reached their target concentration of 1.5E7 cells/ml. A control experiment was conducted, in which the temperature remained at 53 °C, ensuring that the cellular physiology and light attenuation were comparable and that the only difference between the hot and cold treatments relative to the control treatment was temperature. Overall design: Heat stress 61°C and cold stress 45°C samples taken at time 0, 0.5hr, 3hr, 10hr, and 24hr. A control experiment, in which the temperature remained at 53 °C samples taken at time 3hr, 10hr, and 24hr. Each sample timepoint consisted of three biological replicates.
Project description:Two small RNA libraries and 2 degradome libraries were constructed from potato tubers stored at room temperature or exposed to cold stress for deep sequencing. Through small RNA sequencing, 53 known miRNAs and 59 novel miRNAs were identified. Seventy genes were identified as miRNA targets by degradome sequencing. Small RNA sequencing and degradome sequencing of control and cold treated Solanum tuberosum tubers
Project description:Plants were acclimated for 4 d at optimal conditions (32/25 oC day/night) in the growth cabinet before initiation of the temperature treatment. For the control (32 oC), cabinet conditions were left unchanged during the treatment period. Due to limited growth cabinet space, plants of a comparative physiological age were transferred to the controlled environment growth cabinet after the control plants had been removed. Well-watered plants were exposed to heat stress by increasing the ambient air temperature to 42 oC (67% RH) during the photoperiod and 25 oC (40 % RH) during the dark period. The third youngest fully expanded leaf of plants at the first square physiological age was sampled for all experiments. Three leaf tissue samples were collected for each genotype under the ambient or hot growth cabinet (12 samples total) at 0.5, 1, 3, and 7 h after initiation of the high temperature stress, where the time 0.5 samples were collected at 0930 h which equated to 3.5 h into the photoperiod. For RNA preparations, whole leaves were excised at the junction of the lamina and petiole, immediately snap frozen in liquid nitrogen and stored at -80oC. Leaves were ground to a fine powder in liquid nitrogen and a 0.1 g sub-sample was taken and total RNA was extracted using a hot borate buffer. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Nicole Cottee. The equivalent experiment is GO12 at PLEXdb.] Overall design: temperature: 32 C - cultivar: Sicala 45(3-replications); temperature: 32 C - cultivar: Sicot 53(3-replications); temperature: 42 - cultivar: Sicala 45(3-replications); temperature: 42 - cultivar: Sicot 53(3-replications)
Project description:Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas Samples of 38 developmental stages from egg to juvenile were analyzed using single-end 49 bp RNA-seq. Two libraries mixed by RNAs from different developmental stages were analyzed using paired-end 90 bp RNA-seq. A total of 11 samples mainly from 8 organs (mantle, gill,adductor muscle, digestive gland, hemocyte, labial palp, female gonad and male gonad) were analyzed using paired-end 90 bp RNA-seq. At the same time, single-end 49 bp RNA-seq was conducted on 61 samples collected from adult oysters subjected to 9 types of environmental stressors (exposure to air, salinity, temperature, and exposure to metals).
Project description:45 genome-wide microarray measurements for 23 mutation accumulation lines grown in YPD liquid culture MA lines obtained by single-colony transfer on YPD plates for 600 generations, starting from a BY4741 derived strain (see Zeyl C, DeVisser JA: Estimates of the rate and distribution of fitness effects of spontaneous mutation in Saccharomyces cerevisiae. Genetics 2001, 157:53–61) Overall design: Two biological replicates for each strain in a common reference design (no dye-swap)
Project description:45 genome-wide microarray measurements for 23 mutation accumulation lines grown in YPD liquid culture MA lines obtained by single-colony transfer on YPD plates for 600 generations, starting from a BY4741 derived strain (see Zeyl C, DeVisser JA: Estimates of the rate and distribution of fitness effects of spontaneous mutation in Saccharomyces cerevisiae. Genetics 2001, 157:53–61) Two biological replicates for each strain in a common reference design (no dye-swap)
Project description:Low temperature is a major abiotic stress that impedes plant growth and development. Brassica juncea is an economically important oil seed crop and is sensitive to freezing stress during pod filling subsequently leading to abortion of seeds. To understand the cold stress mediated global perturbations in gene expression, whole transcriptome of B. juncea siliques that were exposed to sub-optimal temperature was sequenced. Manually self-pollinated siliques at different stages of development were subjected to either short (6 h) or long (12 h) durations of chilling stress followed by construction of RNA-seq libraries and deep sequencing using Illumina’s NGS platform. De-novo assembly of B. juncea transcriptome resulted in 133641 transcripts, whose combined length was 117 Mb and N50 value was 1428 bp. We identified 13342 differentially regulated transcripts by pair-wise comparison of 18 transcriptome libraries. Hierarchical clustering along with Spearman correlation analysis identified that the differentially expressed genes segregated in two major clusters representing early (5-15 DAP) and late stages (20-30 DAP) of silique development. Further analysis led to the discovery of sub-clusters having similar patterns of gene expression. Two of the sub-clusters (one each from the early and late stages) comprised of genes that were inducible by both the durations of cold stress. Comparison of transcripts from these clusters led to identification of 283 transcripts that were commonly induced by cold stress, and were referred to as ‘core cold-inducible’ transcripts. Additionally, we found that 689 and 100 transcripts were specifically up regulated by cold stress in early and late stages, respectively. We further explored the expression patterns of gene families encoding for transcription factors (TFs), transcription regulators (TRs) and kinases, and found that cold stress induced protein kinases only during early silique development. We validated the digital gene expression profiles of selected transcripts by qPCR and found a high degree of concordance between the two analyses. To our knowledge this is the first report of transcriptome sequencing of cold-stressed B. juncea siliques. The data generated in this study would be a valuable resource for not only understanding the cold stress signaling pathway but also for introducing cold hardiness in B. juncea. Overall design: mRNA-seq profilling of cold stressed Brassica juncea silique, Various development stages ( 5, 10, 15, 20, 25 and 30 DAP) of siliques were taken, 18 samples generated from two different durations of stress (6h, 12h) with their respective control (C).
Project description:Low temperature is one of the major abiotic stresses limiting rice growth and productivity, it is urgent to reveal the genetic and molecular mechanisms of plant responses to low temperature stress and to search for useful genetic resources for improving low-temperature tolerance. the 8 accessions from China Core Collection include 4 cold tolerance accessions, 3 sensitivity accessions and 1 intermediate type accession. We used microarrays to detail variation of the gene expression after cold treatment and screen more cold-response genes in rice. Overall design: In order to getting more understanding of gene expression after cold treatment in rice seedling stage, we applied 8 accessions by cold stress screening in this Affymetrix microarrays, and each accession include 3 time-points samples: (1) before the cold treatment; (2) 6 hours after the cold treatment; (3) 24 hours after the cold treatment.
Project description:Using transcriptomics, we show that Symbiodinium acclimation to elevated temperature involves up-regulated expression of meiosis genes followed by up-regulated expression of numerous reactive oxygen species scavenging genes and molecular chaperone genes. Our study connects Symbiodinium transcriptional regulation with physiological heat stress responses as well as known bleaching responses of corals harboring these same Symbiodinium. By uncovering these critical links, we greatly advance understanding of the bleaching susceptibility of corals, which is a key process responsible for global coral reef health. Overall design: We analyzed gene regulation in response to heat stress by two Symbiodinium C1 populations with contrasting thermal tolerances and bleaching thresholds. The thermo-sensitive South Molle (SM) Symbiodinium population and thermo-tolerant Magnetic Island (MI) Symbiodinium population were cultured in filtered seawater supplemented with Daigo IMK (Wako Pure Chemical Industries, Ltd.). Light was provided at an intensity of 30 µmol quanta m^-2 s^-1 (Crompton 36W cool white fluorescent tubes, 4000 K) with a 12:12 h light:dark cycle. For this study, 50 ml (~1 x 10^6 cells/ml) of each population were added to eight replicate culture flasks per population (n=4 for each temperature treatment). Two flasks per population were randomly assigned to each of four experimental incubators and acclimated at 27°C. After 10 days of acclimation, fresh media was supplied to the cultures. After an additional four days of acclimation (two weeks of acclimation total), two incubators were ramped on day 0 at 0.5°C/h to 32°C for the heat stress temperature treatment, while two incubators remained at 27°C. Temperature and light intensity in the incubators were monitored with HOBO data loggers. Cultures remained in exponential growth phase, determined by the average of three replicate haemocytometer counts for each sample measured throughout the experiment. Transcriptomes were sampled on day -1 (pre-heating), 9, and 13. SM_min250_nr.fasta: South Molle population de novo transcriptome, non-redundant transcripts (min transcript length 250 bp) SM_transcriptome.fasta: preliminary South Molle population de novo transcriptome (min transcript length 150 bp) MI_min250_nr.fasta: Magnetic Island population de novo transcriptome, non-redundant transcripts (min transcript length 250 bp) MI_transcriptome.fasta: preliminary Magnetic Island population de novo transcriptome (min transcript length 150 bp) Trinity_SM_min250nr_annotation_report.complete.5.xls: SM transcriptome annotation spreadsheet Trinity_MI_min250nr_annotation_report.complete.5.xls: MI transcriptome annotation spreadsheet day*nr.counts.txt: gene count matrix across samples
Project description:mRNA profiling of CD34+ human cord blood-derived cell treated with UM171, SR1 or both Overall design: mRNA profiles of CD34+ human cord blood-derived cell treated with DMSO (control), SR1 [500nM], UM171 [35nM] or combination SR1 [500nM]+ UM171 [35nM] for 30min, 3hr, 12hr, 24hr, 48hr, 72hr were generated by deep sequencing
Project description:We observed the expression profile of the total mRNA of wild-type of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 45˚C compared with that of 70˚C. Keywords: Growth temperature Overall design: Wild-type T. thermophilus HB8 strain was pre-cultured at 70˚C for 5 h in 5 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.5 with NaOH. The cells (5 ml) were inoculated into 0.30 liter of the same medium and then cultivated at 70˚C. At the Abs600 =0.8 (0min), this culture was divided into two flasks. Then, equal volume of cold medium (4˚C) was added and the temperature were shifted down to 45˚C. Hot medium (70˚C) was added to the other flask. Cells were collected at 0.5 min and 10 min after temperature shift in the equal volume of 100% ice-cold ethanol, and then crude RNA was extracted. In order to compare mRNA expression in the wild-type strain between 45˚C and 70˚C, the expression of each mRNA at each time point was analyzed on a GeneChip as described for each sample in this website.