90 k whole genome microarray  (CombiMatrix)

Journal: Plant Cell Reports

Article Title: Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella

doi: 10.1007/s00299-021-02794-2

Figure Lengend Snippet: Time series of DEGs in Physcomitrella WT protoplasts 1 h, 4 h, 6 h, 24 h and 72 h after transfection compared to freshly isolated (0 h) protoplasts based on microarray data. DEGs are filtered for q < 0.05. ( a ) Number of DEGs at each time-point. Two maxima of DEGs are apparent after 4 h and 24 h, respectively. ( b ) Overlap of DEGs from each time-point. ( c ) Significantly enriched biological process GO terms ( p < 0.005, q < 0.2). The word size scales with the negative log2 of the adjusted p value

Article Snippet: The microarray experiments were performed with a 90 K whole genome microarray (Combimatrix Corp., Mukilteo, WA, USA) as described previously (Beike et al. ; Kamisugi et al. ; Wolf et al. ).

Techniques: Transfection, Isolation, Microarray

Journal: Plant Cell Reports

Article Title: Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella

doi: 10.1007/s00299-021-02794-2

Figure Lengend Snippet: Number of genes being upregulated or downregulated in protoplasts 4 h and 24 h after transfection as well as protonema (PN) compared to freshly isolated protoplasts (0 h). ( a ) The number of DEGs identified in one haploid line (Haploid A, brown) and in one diploid line (Diploid A, blue). DEGs are combined from identification in the microarray data (filtered for a |log2 fold change|> 1 and p < 0.001) and the SuperSAGE data (filtered for a GFOLD(0.01) value of < −1 or > 1). ( b ) Overlap between the upregulated genes at 24 h in the haploid line with the upregulated genes at 24 h in the diploid line. ( c ) Overlap between the downregulated genes at 24 h in the haploid line with the downregulated genes at 24 h in the diploid line

Article Snippet: The microarray experiments were performed with a 90 K whole genome microarray (Combimatrix Corp., Mukilteo, WA, USA) as described previously (Beike et al. ; Kamisugi et al. ; Wolf et al. ).

Techniques: Transfection, Isolation, Microarray

Journal: Plant Cell Reports

Article Title: Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella

doi: 10.1007/s00299-021-02794-2

Figure Lengend Snippet: Number of DEGs between diploid and haploid cells at different time-points after transfection

Article Snippet: The microarray experiments were performed with a 90 K whole genome microarray (Combimatrix Corp., Mukilteo, WA, USA) as described previously (Beike et al. ; Kamisugi et al. ; Wolf et al. ).

Techniques: Microarray

Journal: Plant Cell Reports

Article Title: Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella

doi: 10.1007/s00299-021-02794-2

Figure Lengend Snippet: Overlap of DEGs identified from pairwise comparison between one haploid (Haploid A) and one diploid (Diploid A) line at different protoplast stages. DEGs were determined by microarray analysis ( a ) and SuperSAGE libraries ( b ) from protoplast samples (grey: freshly isolated protoplasts (0 h), green: protoplasts 4 h after transfection, purple: protoplasts 24 h after transfection. DEGs from the microarray experiment were determined with the Expressionist Analyst Pro software and were filtered for |log2 fold change|> 1 and p < 0.001. The SuperSAGE data analysis was performed with GFOLD and DEGs were filtered for a GFOLD(0.01) value of < − 1 or > 1

Article Snippet: The microarray experiments were performed with a 90 K whole genome microarray (Combimatrix Corp., Mukilteo, WA, USA) as described previously (Beike et al. ; Kamisugi et al. ; Wolf et al. ).

Techniques: Comparison, Microarray, Isolation, Transfection, Software