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DNA microarray data from transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

ABSTRACT: DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. But the distribution of differentially expressed genes in GM crops remains unclear. So the results of microarray analysis might be invalid for assessment of unintended effects if differentially expressed genes are extremely distributed. We used microarrays to study the distribution pattern of differentially expressed genes in HH1 at different developmental stages and environmental conditions.

ORGANISM(S): Oryza sativa

PROVIDER: GSE33204 | GEO | 2011/10/26

SECONDARY ACCESSION(S): PRJNA149257

REPOSITORIES: GEO

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DNA microarray data from transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

Project description:DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. But the distribution of differentially expressed genes in GM crops remains unclear. So the results of microarray analysis might be invalid for assessment of unintended effects if differentially expressed genes are extremely distributed. We used microarrays to study the distribution pattern of differentially expressed genes in HH1 at different developmental stages and environmental conditions. Samples were collected from both HH1 and MH63 at different developmental stages and environmental conditions and were used for RNA extraction and hybridization on Affymetrix microarrays. We selected differentially expressed genes, common differentially expressed genes and common significantly changed pathways hoping to clarify the distributions of differentially expressed genes in HH1.

2011-10-25 | E-GEOD-33204 | biostudies-arrayexpress

DNA microarray data from root of transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

Project description:DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. However, unintended effects of GM plants in leaves through DNA microarray analysis has many researches, but research of unintended effects of GM plants of the underground portion has few. In this study, DNA microarray analysis was used to detect DEG in underground portions between transgenic rice HH1 and its non-transgenic control MH63. We used microarrays to study unintended effects in root of transgenic rice Huahui 1. Samples were collected from root of HH1 and MH63 at 30-day old and were used for RNA extraction and hybridization on Affymetrix microarrays. We selected diferentially expressed genes and common significantly changed pathways hoping to as a clue to investigate unintended effects of HH1 root.

2013-10-16 | E-GEOD-46086 | biostudies-arrayexpress

DNA microarray data from root of transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

2013-10-16 | GSE46086 | GEO

ATAC-seq of YB5 cells treated with HH1

Project description:ATAC-seq was performed after YB5 cells were treated with DMSO or HH1

2018-10-26 | GSE113608 | GEO

RNA-seq of YB5 cells treated with HH1

Project description:RNA-seq was performed after YB5 cells were treated with DAC, HH1 or the combination of the two. RNA-seq was also perfomed after viral transduction using a TET-off dnCDK9 construct

2018-10-26 | GSE104837 | GEO

Shotgun proteomics reveal differential proteins in herbicide-tolerant, conventional, and organic soybean seeds

Project description:The nutritional similarities between herbicide-tolerant genetically modified (GM) crops and non-GM counterparts are used as scientific evidence to show GM crops are substantially equivalent and safe and nutritious to non-GM. A previous study demonstrated substantial non-equivalence in ready-to-market soybeans obtained from 31 samples from Iowa, USA and discriminated GM, non-GM conventionally farmed and organic soybean. In the present study, by using high-resolution tandem mass spectrometry (HRMS) coupled with high-throughput proteomics and bioinformatic analyses, the same 31 individual soybean samples were investigated. Our results show that proteomic profiles of GM, conventionally, and organically farmed soybean samples were different. Differentially expressed proteins were found that can be used as markers to separate conventionally and organically farmed soybean seeds. Our data indicate that HRMS coupled with bioinformatic analyses provide a powerful platform to probe the equivalence of GM with non-GM material in food and feeding stuff.

2022-06-08 | MSV000089618 | MassIVE

DNA methylation analysis of colorectal cancer SW48/YB5 cell line treated with the HH1 compound

Project description:YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving expression of a GFP reporter. The cells were treated with 10 micromolar concentration of the HH1 compound or with DMSO as a control. Reduced representation bisulfite sequencing (RRBS) was performed after the treatment to analyze DNA methylation at CpG sites.

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ATAC-seq of YB5 cells treated with HH1

Project description:ATAC-seq of YB5 cells treated with HH1

| PRJNA453383 | ENA

RNA-seq of YB5 cells treated with HH1

Project description:RNA-seq of YB5 cells treated with HH1

| PRJNA413957 | ENA

DNA microarray data from transgenic rice KMD and its parent XS11

Project description:KMD is genetically engenered to be highly resistant to lepidopteran pests through expressing a synthetic cry1Ab gene and its parent non-transgenic rice is Xiushui 11 (XS11). Many unintended effects have been discovered in KMD. We used microarrays to study the molecular basis for unintended effects of KMD rice. Samples were collected from both KMD and XS11 for RNA extraction and hybridization on Affymetrix microarrays. We selected differentially expressed genes hoping to clarify the molecular basis for unintended effects in KMD.

2011-10-25 | E-GEOD-33203 | biostudies-arrayexpress

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