Microarray of young shoot of Populus trichocarpa under abiotic stresses
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus sp. Populus trichocarpa
PROVIDER: GSE124496 | GEO | 2018/12/30
REPOSITORIES: GEO
Similar Datasets
Project description:To understand how CFIm25, an mRNA 3' processing regulator, affects the global poly(A+) RNAs profiling in hESCs (H9 cell line). We carried out poly(A+)-seq in control (2 samples) and CFIm25 KD (3 samples) hESCs.Using a cutoff value (P<0.05, fold change>1), in total, 577 differentially expressed genes (268 down-regulated genes and 309 up-regulated genes) were found upon CFIm25 KD, and the number of down-regulated genes and up-regulated genes were 84 and 128 respectively if using the cutoff value (P<0.05, fold change>2).
2022-04-21 | GSE176327 | GEO
Project description:Dibenzo[a,h]anthracene DB[a,h]A is a polycyclic aromatic hydrocarbon potent carcinogen. Few studies have investigated the role of DB[a,h]A on mRNA and miRNA expression. In this study a 10-week old male MutaTM Mouse were exposed to 6.25, 12.5, and 25 mg/kg/day DB[a,h]A by oral gavage for 28 consecutive days. DNA adducts were detected in the livers at each DB[a,h]A dose tested, and a dose-dependent increase in lacZ mutants was observed in the same samples. MAANOVA analysis revealed minor changes in the mRNA expression for the two lowest doses. Differential expression of 19 up-regulated and 22 down-regulated transcripts with fold-change > 1.5 (FDR-adjusted P < 0.05) were identified in the 6.25 mg/kg/day DB[a,h]A treatment group. For the 12.5 mg/kg/day treatment group 13 transcripts were up-regulated and 32 down-regulated (FDR-adjusted P < 0.05 and fold-change > 1.5). Major effect on mRNA expression resulted from exposure to the highest dose (25 mg/kg/day) of DB[a,h]A with 135 up-regulated and 104 down-regulated genes with fold-change > 1.5 (FDR-adjusted P < 0.05). The significantly regulated genes are involved in circadian rhythm, drug metabolism, glucose metabolism, cholestrol and lipid metabolism, immune response, cell cycle, and apoptosis. We also investigated miRNA response to the three doses of DB[a,h]A. MiRNA expression was relatively unaffected. Only miR-34a showed significant (FDR-adjusted P < 0.05) up-regulation with a fold change above 1.3-fold.
2013-07-02 | GSE35215 | GEO
Project description:Dibenzo[a,h]anthracene DB[a,h]A is a polycyclic aromatic hydrocarbon potent carcinogen. Few studies have investigated the role of DB[a,h]A on mRNA and miRNA expression. In this study a 10-week old male MutaTM Mouse were exposed to 6.25, 12.5, and 25 mg/kg/day DB[a,h]A by oral gavage for 28 consecutive days. DNA adducts were detected in the livers at each DB[a,h]A dose tested, and a dose-dependent increase in lacZ mutants was observed in the same samples. MAANOVA analysis revealed minor changes in the mRNA expression for the two lowest doses. Differential expression of 19 up-regulated and 22 down-regulated transcripts with fold-change > 1.5 (FDR-adjusted P < 0.05) were identified in the 6.25 mg/kg/day DB[a,h]A treatment group. For the 12.5 mg/kg/day treatment group 13 transcripts were up-regulated and 32 down-regulated (FDR-adjusted P < 0.05 and fold-change > 1.5). Major effect on mRNA expression resulted from exposure to the highest dose (25 mg/kg/day) of DB[a,h]A with 135 up-regulated and 104 down-regulated genes with fold-change > 1.5 (FDR-adjusted P < 0.05). The significantly regulated genes are involved in circadian rhythm, drug metabolism, glucose metabolism, cholestrol and lipid metabolism, immune response, cell cycle, and apoptosis. We also investigated miRNA response to the three doses of DB[a,h]A. MiRNA expression was relatively unaffected. Only miR-34a showed significant (FDR-adjusted P < 0.05) up-regulation with a fold change above 1.3-fold.
2013-07-02 | GSE35195 | GEO
Project description:Dibenzo[a,h]anthracene DB[a,h]A is a polycyclic aromatic hydrocarbon potent carcinogen. Few studies have investigated the role of DB[a,h]A on mRNA and miRNA expression. In this study a 10-week old male MutaTM Mouse were exposed to 6.25, 12.5, and 25 mg/kg/day DB[a,h]A by oral gavage for 28 consecutive days. DNA adducts were detected in the livers at each DB[a,h]A dose tested, and a dose-dependent increase in lacZ mutants was observed in the same samples. MAANOVA analysis revealed minor changes in the mRNA expression for the two lowest doses. Differential expression of 19 up-regulated and 22 down-regulated transcripts with fold-change > 1.5 (FDR-adjusted P < 0.05) were identified in the 6.25 mg/kg/day DB[a,h]A treatment group. For the 12.5 mg/kg/day treatment group 13 transcripts were up-regulated and 32 down-regulated (FDR-adjusted P < 0.05 and fold-change > 1.5). Major effect on mRNA expression resulted from exposure to the highest dose (25 mg/kg/day) of DB[a,h]A with 135 up-regulated and 104 down-regulated genes with fold-change > 1.5 (FDR-adjusted P < 0.05). The significantly regulated genes are involved in circadian rhythm, drug metabolism, glucose metabolism, cholestrol and lipid metabolism, immune response, cell cycle, and apoptosis. We also investigated miRNA response to the three doses of DB[a,h]A. MiRNA expression was relatively unaffected. Only miR-34a showed significant (FDR-adjusted P < 0.05) up-regulation with a fold change above 1.3-fold. RNA samples from 5 control and 4-5 mice per treatment group (6.25mg/kg, 12.50mg/kg, and 25mg/kg) containing 100 ng were labelled using AgilentM-bM-^@M-^Ys miRNA complete labelling and Hyb Kit (Agilent Tech, Mississauga, ON, Canada).
2013-07-02 | E-GEOD-35195 | biostudies-arrayexpress
Project description:A total number of 1,511 probe sets in the bone marrow showed at least two-fold changes with FDR < 0.05, of which 256 probe sets had over four-fold changes. A group of 63 genes in the bone marrow of NDLD mice had more than a 4-fold change with FDR < 0.0001. From 503 genes encoding proteins with ITIM motif that binds to Ptpn6, 109 were up-regulated and 83 were down-regulated.
2015-09-30 | GSE73592 | GEO
Project description:Dibenzo[a,h]anthracene DB[a,h]A is a polycyclic aromatic hydrocarbon potent carcinogen. Few studies have investigated the role of DB[a,h]A on mRNA and miRNA expression. In this study a 10-week old male MutaTM Mouse were exposed to 6.25, 12.5, and 25 mg/kg/day DB[a,h]A by oral gavage for 28 consecutive days. DNA adducts were detected in the livers at each DB[a,h]A dose tested, and a dose-dependent increase in lacZ mutants was observed in the same samples. MAANOVA analysis revealed minor changes in the mRNA expression for the two lowest doses. Differential expression of 19 up-regulated and 22 down-regulated transcripts with fold-change > 1.5 (FDR-adjusted P < 0.05) were identified in the 6.25 mg/kg/day DB[a,h]A treatment group. For the 12.5 mg/kg/day treatment group 13 transcripts were up-regulated and 32 down-regulated (FDR-adjusted P < 0.05 and fold-change > 1.5). Major effect on mRNA expression resulted from exposure to the highest dose (25 mg/kg/day) of DB[a,h]A with 135 up-regulated and 104 down-regulated genes with fold-change > 1.5 (FDR-adjusted P < 0.05). The significantly regulated genes are involved in circadian rhythm, drug metabolism, glucose metabolism, cholestrol and lipid metabolism, immune response, cell cycle, and apoptosis. We also investigated miRNA response to the three doses of DB[a,h]A. MiRNA expression was relatively unaffected. Only miR-34a showed significant (FDR-adjusted P < 0.05) up-regulation with a fold change above 1.3-fold. Individual total RNA (200 ng) from 4-5 mice per treatment group (control, 6.25 mg/kg, 12.5mg/kg, and 25mg/kg) and universal reference total RNA (Stratagene, Mississauga, ON, Canada) was used to synthesize double stranded cDNA. Agilent mouse 8 x 60 K oligonucleotide microarrays were used to assess global gene expression in response to 6.25, 12.50, and 25 mg/kg DB[a,h]A treatment
2013-07-02 | E-GEOD-35215 | biostudies-arrayexpress
Project description:NGS was performed to detect human circRNAs. We found many upregulated and downregulated circRNAs in GD patients. Through high-throughput sequencing technology, 23215 upregulated and 13715 down-regulated circRNAs were detected between gd patient group and the healthy control group. Of the 218 circRNAs with significant difference, 359 were up-regulated and 309 were down-regulated.
2022-09-01 | GSE197637 | GEO
Project description:RNA-seq analysis were applied to elucidate the transcriptional differences of PHF8 wild-type and PHF8 knockout TRAMP mouse. A total of 2,092 differentially expressed genes (Fold Change > 2, or Fold Change＜0.5; FDR < 0.05) with 623 down- and 1469 up-regulated genes were identifed in Phf8-KO TRAMP mice.
2020-09-26 | GSE157621 | GEO
Project description:Purpose: The goal of this study are to reveal the internal mechanism of silicon increased Glycyrrhiza uralensis Fisch. seedlings drought-tolerance,salt-tolerance and salt-drought tolerance by RNA-Seq. Methods: mRNA profiles of Glycyrrhiza uralensis Fisch. Seedling in eight treatment: control treatment with or without silicon,salt treatment with or without silicon,drought treatment with or without silicon,salt-drought treatment with or without silicon. Each treatment group sequenced the aerial (stems, leaves, buds and all the above ground parts) and underground parts (roots and all the underground parts) respectively Results:A total of 48 samples were sequenced and 372.37GB of clean data was acquired. The clean data of every sample reached 5.96GB, and the percentage of Q30 base was 94.63% or above. Clean reads of each sample were sequentially aligned with the specified reference genome, and alignment efficiency ranged from 85.27% to 92.66%. Therefore, the transcriptome data of samples were obtained with a high correct rate and good genomic coverage.Results of sequencing analysis showed that compared with CK group, there were 1426 DEGs (771 up-regulated and 655 down-regulated), 1386 DEGs (571 up-regulated and 815 down-regulated) and 4192 DEGs (1668 up-regulated and 2524 down-regulated) in aerial part, and 1462 DEGs (730 up-regulated and 732 down-regulated), 2212 DEGs (939 up-regulated and 1273 down-regulated) and 3735 DEGs (1768 up-regulated and 1986 down-regulated) in underground part of D, S and SD group respectively. Conclusions: Our study help to better understand the underlying molecular mechanisms of silicon improve the drought-tolerance,salt-tolerance and salt-drought tolerance of G. uralensis.
2022-02-21 | GSE197004 | GEO
Project description:We wanted to correlate the protein cargo of secreted exosomes with gene expression pattern in B16-F1 and B16-F1R2. For that purpose, we performed RNA sequencing analysis of B16-F1, B16-F1R2 and B16-F1R2L (Fig.1E). We identified >3000 genes significantly up-regulated and >1000 significantly down-regulated in B16-F1R2 model compared to B16-F1, using a false discovery rate (FDR) of 0.05.
2021-07-28 | GSE150221 | GEO