De novo assembly and transcriptome analysis of Ocimum americanum var. pilosum under low temperature
Ontology highlight
ABSTRACT:
ORGANISM(S): Ocimum americanum
PROVIDER: GSE68980 | GEO | 2015/05/19
SECONDARY ACCESSION(S): PRJNA284256
REPOSITORIES: GEO
Similar Datasets
Project description:One-month-old Ocimum americanum var. pilosum plants were treated with 4 ºC for 12 hours. Total RNAs were extracted from these chilling-treated plant leaves and untreated ones. Two seperate replicates of total RNA samples are from different individuals. The genomic DNA residual in each sample was removed by DNase I digestion. Our goal is to get a more particlular knowledge of transcriptional regulation after chilling treatment in such a chilling-hypersensitive herb.
2015-05-19 | E-GEOD-68980 | biostudies-arrayexpress
Project description:253 genes showed more than 4-fold up- or down-regulated expressions by poly (I:C) at 15 ºC and 25 ºC. Fish were treated with poly(I:C) and reared at 15 ºC and 25 ºC and isolation of total RNA from spleen of the fish at 3 and 24 hours after the treatment.
2015-09-08 | E-GEOD-66692 | biostudies-arrayexpress
Project description:Epigenetic regulation of mutually exclusive transcription within the var gene family is important for infection and pathogenesis of the malaria parasite Plasmodium falciparum. var genes are kept transcriptionally silent via heterochromatic clusters located at the nuclear periphery; however, only a few proteins have been shown to play a direct role in var gene transcriptional regulation. Importantly, the chromatin components that contribute to var gene nuclear organization remain unknown. Here, we adapted a CRISPR-based immunoprecipitation-mass spectrometry approach for de novo identification of factors associated with specific transcriptional regulatory sequences of var genes. Tagged, catalytically inactive Cas9 (“dCas9”) was targeted to var gene promoters or introns, cross-linked, and immunoprecipitated with all DNA, proteins, and RNA associated with the targeted locus. Chromatin immunoprecipitation followed by sequencing demonstrated that genome-wide dCas9 binding was specific and robust. Proteomics analysis of dCas9-immunoprecipitates identified specific proteins for each target region, including known and novel factors such as DNA binding proteins, chromatin remodelers, and structural proteins. We also demonstrate the ability to immunoprecipitate RNA that is closely associated to the targeted locus. Our CRISPR/dCas9 study establishes a new tool for targeted purification of specific genomic loci and advances understanding of virulence gene regulation in the human malaria parasite.
2020-05-01 | GSE129397 | GEO
Project description:Introduction : By mid-century, global atmospheric carbon dioxide concentration ([CO2]) is predicted to reach 600 umol mol-1 with global temperatures rising by 2ºC. Rising [CO2] and temperature will alter the growth and productivity of major food and forage crops across the globe. Although the impact is expected to be greatest in tropical regions, the impact of climate-change has been poorly studied in those regions. Objectives : This experiment aimed to understand the effects of elevated [CO2] (600 umol mol-1) and warming (+ 2°C), singly and in combination, on Panicum maximum Jacq. (Guinea grass) metabolite and transcript profiles. Methods: We created a de novo assembly of the Panicum maximum transcriptome. Leaf samples were taken at two time points in the Guinea grass growing season to analyze transcriptional and metabolite profiles in plants grown at ambient and elevated [CO2] and temperature, and statistical analyses were used to integrate the data. Results: The MiSeq library was quantified by qPCR and sequenced on one MiSeq flowcell for 301 cycles using paired-end sequencing. HiSeq paired-end sequencing was done with four quantified libraries per treatment which were pooled in equimolar concentration, and sequenced on two lanes for 161 cycles. The final read lengths for MiSeq and HiSeq were 300 nt and 160 nt in length. A total of 635,649,277 reads were assembled from the MiSeq/HiSeq pools. Quality control for reads generated from sequencing was performed using FastQC. Quality reads were used to perform de novo transcriptome assembly using Trinity. The initial assembly consisted of 187,216 genes. A filter was applied to keep only those genes that had at least 10 reads (across the 4 replicates) for an individual treatment. The resulting transcriptome contained 45,073 genes and reads. Functional annotation of the genes was done by using BLAST against Arabidopsis thaliana, Zea mays, and Setaria italica.
2018-11-07 | GSE122194 | GEO
Project description:The P. falciparum genome is equipped with several subtelomeric gene families that are implicated in parasite virulence and immune evasion. The members of these gene families are uniformly positioned within heterochromatic domains of the genome and are thus subject to variegated expression. The best-studied example is that of the var gene family encoding the major parasite virulence factor P. falciparum erythrocyte membrane protein 1 (PfEMP1). Transcriptional regulation of other subtelomeric gene families and their role in parasite biology is much less understood. Here, we investigated the mode of transcriptional control of var, rif, stevor, phist and pfmc-2tm families by comparative genome-wide transcriptional profiling of transgenic parasite lines. Our results establish a clear functional distinction between var and non-var transcriptional control mechanisms. Unlike var promoters, we find that promoters of non-var families are not silenced by default. Moreover, we show that mutually exclusive transcription is unique to the var gene family.
2011-09-02 | GSE31829 | GEO
Project description:Abaca (Musa textilis Née), an indigenous crop to the Philippines, is known to be the source of the strongest natural fiber. Despite its huge economic contributions, research on crop improvement is limited due to the lack of genomic data. In this study, the whole genome of the abaca var. Abuab was sequenced using Illumina Novaseq 6000 and Pacific Biosciences Single-Molecule Real-Time Sequel. The genome size of Abuab was estimated to be 616 Mbp based on total k-mer number and volume peak. Its genome was assembled at 65× depth, mapping 95.28% of the estimated genome size. BUSCO analysis recovered 78.2% complete BUSCO genes. A total of 33,277 gene structures were predicted which is comparable to the number of predicted genes from recently assembled Musa spp. genomes. A total of 330 Mbp repetitive elements were also mined, accounting to 53.6% of the genome length. Here we report the sequencing and genome assembly of the abaca var. Abuab that will facilitate gene discovery for crop improvement and an indispensable source for genetic diversity studies in Musa.
| S-EPMC8392402 | biostudies-literature
Project description:Circular RNA raw sequence reads of Camellia sinensis var. sinensis under chilling stress
| PRJNA893865 | ENA
Project description:253 genes showed more than 4-fold up- or down-regulated expressions by poly (I:C) at 15 ºC and 25 ºC.
2015-09-08 | GSE66692 | GEO
Project description:Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars, B. juncea and B. nigra, for salinity tolerance. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52. We report transcriptome sequencing of two-weeks-old seedlings of B. juncea var. CS52 under normal growth conditions (CTRL) and in response to salinity stress (SS) using Illumina paired-end sequencing
2015-02-28 | E-GEOD-66389 | biostudies-arrayexpress
Project description:In Drosophila, Piwi-induced transcriptional repression is associated with the establishment of repressive chromatin marks by the histone methyltrasferase SetDB1, however how the Piwi/piRNA complex recruits this effector to chromatin targets is poorly understood. We identified a new player in piRNA-guided transcriptional silencing encoded by the Su(var)2-10 gene. Su(var)2-10 is required for transcriptional silencing and deposition of repressive chromatin marks on transposons and it physically associates with the Piwi/piRNA target recognition complex. Recruitment of Su(var)2-10 to a target locus in a piRNA-independent fashion induces transcriptional repression and deposition of the H3K9 trimethyl mark by the histone methyltransferase dSetDB1/Eggless. Su(var)2-10 belongs to a conserved family of proteins that function as SUMO E3 ligases and we found that the SUMO pathway is essential for the repressive function of Su(var)2-10 and for transcriptional repression of transposons. Together, our data identifies Su(var)2-10 as an essential component of the piRNA-induced transcriptional silencing pathway that links the target recognition complex to the silencing effector and reveals a novel role of SUMO modification in the piRNA-induced repression.
2019-12-18 | GSE115277 | GEO