Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-30095
PROVIDER: PRJNA155185 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome-wide Identification of SHR Direct Targets Using a Custom Agilent Promoter Array
| PRJNA126153 | ENA
Project description:ChIP-chip analysis was used to identify direct targets of the transcription factor SCR SCARECROW (SCR) is a key regulatory of radial patterning and stem cell renewal in the primary root. We have shown in previous studies that SCR is a direct transcriptional regulator in Arabidopsis thaliana. With the aim of understanding the molecular pathway acting downstream of SCR in primary root development, we identified SCR direct targets at the genome-wide level in primary roots.To do this we designed a promoter microarray (chip) for Arabidopsis containing probes tiling the intergenic regions, first intron, and 3’UTR of all annotated genes. We performed Chromatin Immunoprecipitation (ChIP) using an antibody to Green Fluorescent Protein (GFP) on roots of transgenic plants expressing a functional fusion protein of SCR and GFP that is driven by the SCR promoter. Our control was performing ChIP in parallel using the same anti-GFP antibody on roots of Columbia-O wild-type plants. DNA recovered from the SCR and wild-type ChIP experiments with Cy5 and Cy3 dye, respectively, and then hybridized to the same microarray. The array was scanned using an Agilent scanner and the signal intensity for each channel was retrieved and normalized by Agilent feature extraction software. Two biological replicates of this ChIP-chip experiment were performed.
2011-11-23 | GSE30104 | GEO
Project description:ChIP-chip analysis was used to identify direct targets of the transcription factor SCR SCARECROW (SCR) is a key regulatory of radial patterning and stem cell renewal in the primary root. We have shown in previous studies that SCR is a direct transcriptional regulator in Arabidopsis thaliana. With the aim of understanding the molecular pathway acting downstream of SCR in primary root development, we identified SCR direct targets at the genome-wide level in primary roots.To do this we designed a promoter microarray (chip) for Arabidopsis containing probes tiling the intergenic regions, first intron, and 3M-bM-^@M-^YUTR of all annotated genes. We performed Chromatin Immunoprecipitation (ChIP) using an antibody to Green Fluorescent Protein (GFP) on roots of transgenic plants expressing a functional fusion protein of SCR and GFP that is driven by the SCR promoter. Our control was performing ChIP in parallel using the same anti-GFP antibody on roots of Columbia-O wild-type plants. DNA recovered from the SCR and wild-type ChIP experiments with Cy5 and Cy3 dye, respectively, and then hybridized to the same microarray. The array was scanned using an Agilent scanner and the signal intensity for each channel was retrieved and normalized by Agilent feature extraction software. Two biological replicates of this ChIP-chip experiment were performed. Two biological replicates of the ChIP-chip experiment were performed using samples isolated from primary roots. Each Agilent array was hybridized with both SCR ChIP and wild-type control samples differentially labeled with Cy5 and Cy3 dye, respectively.
2011-11-23 | E-GEOD-30104 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE30091: Expression analysis of the effect of protoplasting and sorting in roots exposed to low pH GSE30095: Expression analysis of root cell types after treatment with low pH GSE30096: Expression analysis of developmental stages of Arabidopsis roots exposed to low pH GSE30097: Time-course expression analysis of the low pH (pH 4.6) response in Arabidopsis whole roots GSE30098: Expression analysis time-course of Arabidopsis roots to sulfur deficiency GSE30099: Expression analysis of root cell types after treatment with sulfur deficient media GSE30100: Expression analysis of developmental stages of Arabidopsis roots exposed to sulfur deficient media GSE30104: Genome-wide identification of SCARECROW (SCR) direct targets using a custom Agilent promoter array Refer to individual Series
2011-11-23 | E-GEOD-30166 | biostudies-arrayexpress
Project description:Identification of Direct Targets of RPX a NAC transcription factor of Arabidopsis thaliana
2014-07-03 | E-GEOD-34837 | ExpressionAtlas
Project description:Identification of WUSCHEL direct targets.
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Project description:Transcription profiling by array of human acute lymphoblastic leukemia and normal haemopoietic samples using Agilent Whole Human Genome Oligo Microarrays
2025-01-23 | E-MTAB-4006 | ExpressionAtlas
Project description:Identification of NLP7 direct targets using ChIP-chip in Arabidopsis thaliana
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Project description:Identification of Direct Targets of SND1 and VND7
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Project description:Identification of Sox3 targets in mouse neural progenitor cells
2015-07-31 | E-GEOD-53760 | ExpressionAtlas