Transcriptomic profiling of E.coli upon toxin expression
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This project involves performing RNA seq on E.coli to characterize the transcriptomic responses triggered by the expression of the toxin. The main goal was to identify genes that become significantly differentially expressed upon toxin induction, providing insights into the molecular pathways affected by toxin activity. Analyzing these transcriptomic changes can help uncover the regulatory mechanisms the bacteria employs in response to toxin induced stress, potentially shedding light on bacterial stress responses, survival strategies, and the broader biological significance of the toxin under investigation.
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2025-12-03
相关数据集
Whole-transcriptome profilings between a pair of HCA7-derived KRAS-wildtype cetuximab sensitive and resistant colon cancer cells from 3D culture. Homo sapiens
We report the results of RNA-Seq and small RNA-Seq from a pair of HCA7-derived, KRAS wildtype CC and CC-CR cultured in 3D. A total of 361 genes showed more than a two-fold change in expression (false-discovery rate [FDR] - adjusted p2, FDR<0.01). Differential expression analysis revealed several novel candidates that may contribute to cetuximab resistance. The whole-transcriptome profilings using cetuximab resistance model from 3D culture provide novel candidates for cetuximab resistance and further functional studies might open the door to a novel understanding of how non-mutational mechanisms mediate cetuximab resistance. Overall design: mRNA and small-RNA profiles of cetuximab sensitive CC and resistant CC-CR from 3D culture were generated by deep sequencing, in triplicate, using Illumina NextSeq 500 sequencer.
NIAID Data Ecosystem30
The Antarctic moss Leptobryum pyriforme transcriptome sequencing
Bryophytes are the dominant flora in the Antarctic continent. They suffer more harmful ultraviolet radiation in Antarctica due to the ozone layer destruction. However, the molecular mechanism of Antarctic moss adaptation to UV-B radiation remains unclear. In the research, the gene transcriptional profiling the Antarctic moss Leptobryum pyriforme under UV-B radiation was conducted by RNA sequencing technology.The differentially expressed genes in Antarctic moss were analyzed by comparing UV-B radiation group and control group.
NIAID Data Ecosystem20
RNA-seq reveals ultrasound-guided renal parenchymal infusion of mesenchymal stem cells in chronic kidney disease rat model
Chronic kidney disease (CKD) is a disease characterized by normal or reduced proteinuria, glomerular filtration rate, progressive damage to glomeruli, tubules, and interstitium. In this study, we performed RNA-seq reveals ultrasound-guided renal parenchymal infusion of mesenchymal stem cells in SD rats animal model in chronic kidney disease. Our results indicate that differential genes in the normal group(n=3) VS CKD group(n=3) and normal group(n=3) VS MSCs treatment group(n=3). Overall design: Transcriptome analysis by high throughput sequencing
NIAID Data Ecosystem00
Transcriptome Analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain (ADG) in Hanwoo Cattle
Purpose: This goal of this study was to explore the skelletal muscle transcriptomic responses in different daily weight gain in Hanwoo Cattle using RNA-Sequencing.
NIAID Data Ecosystem00
Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO L-02 cells. Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO L-02 cells
Purpose: We idenficied a circRNA, circBNC2, that was downregulated during hepatocytes injury. To study the function of circBNC2, we performed CRISPR-Cas9 to knock out circBNC2 in L-02 (a well recognized human hepatocytes) cells. Next-generation Sequencing was used to identified the differentially expressed mRNA between circBNC2-KO L-02 cells and wild-type L-02 cells. Overall design: Methods: mRNA profiles of circBNC2-KO cells or wild-type cells were generated by deep sequencing, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays.
NIAID Data Ecosystem60
Additional file 9: Table S9. of Transcriptomic analysis of differentially expressed genes in the floral transition of the summer flowering chrysanthemum
Genes differentially transcribed in the comparison in the comparison L1 vs S1. Criteria as given in Additional file 4: Table S4. (XLS 333Â kb)
NIAID Data Ecosystem30
Rosa persica sequencing
Transcriptome of petal blotch and non-blotch during flower development of Rosa persica were performed to identify the genes responsible for the blotch formation
NIAID Data Ecosystem10
Transcription profiling of Arabidopsis plants overexpressing SsCBF1
Solanum lycopersicoides (LA2408), collected at higher altitudes (up to 3600 meters) than any of other solanum species, is a wild nightshade distant-allied to cultivated tomato. Many traits of Solanum lycopersicoides including cold tolerance, resistance to virus diseases and insect pests were previously confirmed. Thus, it is an ideal candidate plant for isolating cold-tolerance-related genes. In this study, we successfully cloned the full-length cDNA of the CBF1 gene from Solanum lycopersicoides which was designated as SsCBF1. In order to investigate the possible functions of SsCBF1 in plant growth and stress responses, we generated transgenic Arabidopsis overexpressing SsCBF1. We employed the RNA-seq approach to identify the differentially expressed genes between the two genotypes. Processing of RNA samples on the Illumina HiSeq 2000 system produced more than 20 million reads, each 100bp in length, encompassing 2.0 Gb of sequence data for each sample which was then mapped to the reference genome. The statistical analysis identified a total of 338 differentially expressed genes between Col-0 (WT) and transgenic Arabidopsis overexpressing SsCBF1 with the criteria of Q-value 2, among which 120 (35.5%) were up-regulated and 218 (64.5%) were down-regulated. Overall design: RNA-sequencing was carried out using one transgenic line (35S:SsCBF1-11) and the Col-0 (WT) plants. Total RNA was isolated with Trizol reagent (Invitrogen, USA) from the aerial parts of 4-week-old seedlings grown in parallel under unstressed conditions. Materials from 20 plants of each genotype were pooled for RNA isolation.
NIAID Data Ecosystem30
Table_1_Transcriptome responses of RNAi-mediated ETH knockdown in Scylla paramamosain at different premolt substages.docx
Ecdysis triggering hormone (ETH) plays an important role in molting, reproduction, and courtship behavior in insects. To investigate the potential downstream pathways and genes of ETH in Scylla paramamosain, RNA interference (RNAi) was conducted on crabs at early (D0) and late (D2) premolt substages, and the transcriptome profiles of each group were compared by RNA sequencing. Real-time quantitative polymerase chain reaction (RT-qPCR) and semiquantitative polymerase chain reaction (RT-PCR) results showed a significant knockdown of ETH at D0 stage, whereas a significant increase was shown conversely in crabs at D2 substage after the injection of dsETH. A total of 242,979 transcripts were assembled, and 44,012 unigenes were identified. Transcriptomic comparison between crabs at D2 and D0 substages showed 2,683 differentially expressed genes (DEGs); these genes were enriched in ribosome and pathways related to transcription factor complex and cell part. Twenty DEGs were identified between dsETH-injected and dsGFP-injected crabs at D0 substage; these DEGs were involved in carbohydrate metabolism, one carbon pool by folate, and chitin binding. Twenty-six DEGs were identified between dsETH-injected and dsGFP-injected crabs at D2 substage; these DEGs were involved in calcium channel inhibitor activity, fat digestion and absorption, and cardiac muscle contraction. RT-qPCR verified the differential expression of the selected genes. In conclusion, crabs at D0 substage are more active in preparing the macromolecular complex that is needed for molting. Moreover, ETH has potential roles in carbohydrate metabolism, one carbon pool by folate, and chitin binding for crabs at D0 substage, while the role of ETH turns to be involved in calcium channel inhibitor activity, fat digestion and absorption, and cardiac muscle contraction at D2 substage to facilitate the occurrence of molting. The selected DEGs provide valuable insight into the role of ETH in the regulation of crustacean molting.
NIAID Data Ecosystem10
Differential gene expression in human keratinocytes cultured on different substrate topographies (S1 and S2) for 1h, 4h and 12h.
Substrate topography has emerged as a novel regulator of cell fate behaviour in keratinocytes (Zijl, Acta Biomater, 2019). Specifically, small circular micropillars (S1) can induce the differentiation of spread cells, and larger triangular substrates (S2) can inhibit differentiation in kerinocytes. Here we investigated the potential molecular mechanisms behind these processes. We chose timepoints previously shown to be associated with differentiation in suspension cultures (Mishra, eLife, 2017), in order to find early regulators of the differentiation process. Our results show a delay in differentiation on S2 substrates and an upregulation of differentiation pathways on S1. Beyond this, no clear mechanistic regulators of the differentiation program were found. Overall design: Bulk RNA sequencing on S1 and S2 substrates after 1h, 4h and 12h of culture on different substrate topographies.
NIAID Data Ecosystem10
Table 3_Human umbilical cord mesenchymal stem cells recover chemotherapy-induced premature ovarian failure.xlsx
BackgroundCurrent therapeutic approaches for premature ovarian failure (POF) are often inadequate in clinical practice and some raise ethical concerns. Human umbilical cord mesenchymal stem cells (hUC-MSCs) have emerged as a preferred option for cell transplantation, attributed to their facile extraction process and minimal immunogenicity. Objective and methodsThis study aimed to elucidate the transcriptomic alterations associated with hUC-MSCs treated in the context of POF mice and to explore their underlying biological mechanisms. POF mice were established via injecting cyclophosphamide (CTX) plus busulfan (BU). Subsequently, ovaries and serum were collected after 1 week for model identification. 4 weeks after hUC-MSCs transplantation, ovaries and serum were collected for experimental analysis. Differentially expressed genes (DEGs) were identified using RNA sequencing (RNA-seq), and their expression levels were validated through reverse transcription quantitative polymerase chain reaction (RT-qPCR). ResultsAfter hUC-MSCs therapy, the number of follicles recovered significantly and the atretic follicles decreased significantly. FSH was reduced, AMH and E2 levels were increased in the treatment group, and comparable to the control group. 343 DEGs were detected in the POF group and the treatment group, including 187 up-regulated genes and 156 down-regulated genes. Our comparative analysis of hUC-MSCs treated with POF samples revealed significant involvement of biological pathways and processes related to cell adhesion, proliferation, apoptosis, inflammatory response and immune response. ConclusionOur research offers a novel perspective on the application of hUC-MSCs for the treatment of POF and establishes a foundation for further exploration of their potential clinical applications.
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Expression of defense related genes in resistance and susceptible tobacco (Nicotiana tabacum) in response to Ralstonia solanacearum infection
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RNAseq genome hits.
Over- and under-transcribed gene sets for strain groups of interest; Genbank CDS list for reference, annotated with some genome island and prophage regions. Protocol for annotation transfer is in S9 File. (XLSX)
Figshare2022-04-04 更新00
Transcriptome sequencing of strong, middle and weak gluten strength wheat. Transcriptome sequencing of strong, middle and weak gluten strength wheat
Here is reported the first study of transcriptome analyses using the Illumina HiSeq 4000 platform for three kinds of wheat (G represents Strong gluten wheat, Z represents middle gluten wheat,R represents weak gluten wheat). The variation of wheat varieties with different gluten content is mainly shown in the content of gluten, flour is divided into high gluten powder ( > 30%), medium gluten powder (26%-30%) and low gluten powder ( < 20%), according to the wet gluten content. In total, over 102.6 Gb clean reads were produced and 114, 621 unigenes were assembled; more than 59,085 unigenes had at least one significant match to an existing gene model. Differentially expressed gene analysis identified 2339 and 2600 unigenes which were expressed higher or lower among strong gluten, middle gluten and weak gluten wheat. After functional annotation and classification, three dominant pathways including protein isomerase, antioxidase activity and energy metabolism, and 410 unigenes related to gluten strength polymerization of wheat were discovered. In strong-gluten wheat, low molecular weight subunit content is higher than weak-gluten wheat, and the activity of cysteine synthase and isomerase is increased, which may promote the cross-linking of low molecular weight protein to high molecular weight protein. Meanwhile, POD enzyme strengthens gluten network and CAT enzyme affects gluten polymerization, along with higher ATPase activity, which will provides energy for protein polymerization reaction in comparison of strong-gluten wheat and weak-gluten wheat. The accuracy of these RNA-seq data was validated by qRT-PCR analysis. These data will extend our knowledge of quality characteristics of wheat and provide a theoretical foundation for molecular mechanism research of wheat. Overall design: Different gluten strength wheat mRNA profiles was generated by RNA-seq, with three biological repeats, using Illumina 4000 platform
NIAID Data Ecosystem30
Trancriptome sequencing in mandarin fish
To reveal the molecular mechanisms of differences in mandarin fish fed with the fresh baits and artificial diets
NIAID Data Ecosystem10
Additional file 24: of Genes, pathways and transcription factors involved in seedling stage chilling stress tolerance in indica rice through RNA-Seq analysis
Table S18. Differentially expressed TF involved at 48âh late response phase of both CSV and CTV genotypes with annotation. (XLS 88 kb)
NIAID Data Ecosystem70
Scotian Shelf Winter Skate_UP-regulated_GO-Terms
Scotian Shelf Winter Skate_Down-regulated_Geno Ontology-Terms >1 fold change in sequencing RPKM
Dryad2016-01-01 更新00
DESeq2 outputs for gene length normalization.
This table contains multiple intra- and inter-species comparisons, contrasting control and drought conditions. (XLSX)
Figshare2025-05-20 更新10
Solanum virginianum Raw sequence reads. Solanum virginianum
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RNA-seq analysis of OsILR3 overexpression plants
Differentially expressed genes regulated by Rhizoctonia solani resistant gene OsILR3
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