 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 23, 2024 |
| Title |
Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Loss-of-function mutant alleles were characterized for 22 maize transcription factors to test the functional relevance of prior yeast-one-hybrid and co-expression gene regulatory network predictions. The transcriptome and phenolic metabolome of these mutants were profiled to document the functional roles of these transcription factors. A subset of the prior gene regulatory network predictions were supported but had limited overall power in predicting changes in gene expression or phenolic compounds. The limitations of testing transcription factor-target predictions with single TF knockouts are discussed.
|
| |
|
| Overall design |
Loss-of-function mutant alleles were isolated for 22 maize transcription factors. Transcriptome profiling by RNA-seq was performed for each TF mutant allele to characterize genome-wide perturbations of expression. Enrichment tests were performed to determine if predicted target genes were enriched for differential expression.
|
| |
|
| Contributor(s) |
Ellison EL, Zhou P, Chu Y, Hermanson P, Grotewold E, Springer NM, Gomez-Cano L, Myers ZA, Abnave A, Gray J, Hirsch CN |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA936808 |
| |
| Submission date |
Oct 23, 2024 |
| Last update date |
Oct 23, 2024 |
| Contact name |
Nathan Springer |
| Organization name |
University of Minnesota
|
| Department |
Plant and Microbial Biology
|
| Lab |
140 Gortner Laboratory
|
| Street address |
1479 Gortner Ave
|
| City |
St Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL24163 |
Illumina HiSeq 4000 (Zea mays) |
| GPL25410 |
Illumina NovaSeq 6000 (Zea mays) |
|
| Samples (113)
|
| GSM8588638 |
baf60.21-m2, tassel stem, biol rep 1 |
| GSM8588639 |
baf60.21-m2, tassel stem, biol rep 2 |
| GSM8588640 |
baf60.21-m2, tassel stem, biol rep 3 |
| GSM8588641 |
bzip76-m2, seedling leaf, biol rep 1 |
| GSM8588642 |
bzip76-m2, seedling leaf, biol rep 2 |
| GSM8588643 |
bzip76-m2, seedling leaf, biol rep 3 |
| GSM8588644 |
bzip76-m3, seedling leaf, biol rep 1 |
| GSM8588645 |
bzip76-m3, seedling leaf, biol rep 2 |
| GSM8588646 |
bzip76-m3, seedling leaf, biol rep 3 |
| GSM8588647 |
c3h42-m1, tassel stem, biol rep 1 |
| GSM8588648 |
c3h42-m1, tassel stem, biol rep 2 |
| GSM8588649 |
c3h42-m1, tassel stem, biol rep 3 |
| GSM8588650 |
e2f13-m1, coleoptile tip, biol rep 1 |
| GSM8588651 |
e2f13-m1, coleoptile tip, biol rep 2 |
| GSM8588652 |
e2f13-m1, coleoptile tip, biol rep 3 |
| GSM8588653 |
e2f19-m1, seedling leaf, biol rep 1 |
| GSM8588654 |
e2f19-m1, seedling leaf, biol rep 2 |
| GSM8588655 |
e2f19-m1, seedling leaf, biol rep 3 |
| GSM8588656 |
e2f19-m2, seedling leaf, biol rep 1 |
| GSM8588657 |
e2f19-m2, seedling leaf, biol rep 2 |
| GSM8588658 |
e2f19-m2, seedling leaf, biol rep 3 |
| GSM8588659 |
gras52-m1, imbibed embryo, biol rep 1 |
| GSM8588660 |
gras52-m1, imbibed embryo, biol rep 2 |
| GSM8588661 |
gras75-m1, imbibed embryo, biol rep 1 |
| GSM8588662 |
gras75-m1, imbibed embryo, biol rep 2 |
| GSM8588663 |
gras75-m1, imbibed embryo, biol rep 3 |
| GSM8588664 |
hsf13-m1, seedling leaf, biol rep 1 |
| GSM8588665 |
hsf13-m1, seedling leaf, biol rep 2 |
| GSM8588666 |
hsf13-m1, seedling leaf, biol rep 3 |
| GSM8588667 |
hsf18-m1, imbibed embryo, biol rep 1 |
| GSM8588668 |
hsf18-m1, imbibed embryo, biol rep 2 |
| GSM8588669 |
hsf18-m1, imbibed embryo, biol rep 3 |
| GSM8588670 |
hsf20-m1, imbibed embryo, biol rep 1 |
| GSM8588671 |
hsf20-m1, imbibed embryo, biol rep 2 |
| GSM8588672 |
hsf20-m1, imbibed embryo, biol rep 3 |
| GSM8588673 |
hsf24-m3, tassel, biol rep 1 |
| GSM8588674 |
hsf24-m3, tassel, biol rep 2 |
| GSM8588675 |
hsf24-m3, tassel, biol rep 3 |
| GSM8588676 |
hsf24-m4, tassel, biol rep 1 |
| GSM8588677 |
hsf24-m4, tassel, biol rep 2 |
| GSM8588678 |
hsf24-m4, tassel, biol rep 3 |
| GSM8588679 |
hsf29-m1, imbibed embryo, biol rep 1 |
| GSM8588680 |
hsf29-m1, imbibed embryo, biol rep 2 |
| GSM8588681 |
hsf29-m1, imbibed embryo, biol rep 3 |
| GSM8588682 |
hsf29-m2, imbibed embryo, biol rep 1 |
| GSM8588683 |
hsf29-m2, imbibed embryo, biol rep 2 |
| GSM8588684 |
hsf29-m2, imbibed embryo, biol rep 3 |
| GSM8588685 |
hsf6-m1, imbibed embryo, biol rep 1 |
| GSM8588686 |
hsf6-m1, imbibed embryo, biol rep 2 |
| GSM8588687 |
hsf6-m1, imbibed embryo, biol rep 3 |
| GSM8588688 |
hsf6-m2, imbibed embryo, biol rep 1 |
| GSM8588689 |
hsf6-m2, imbibed embryo, biol rep 2 |
| GSM8588690 |
hsf6-m2, imbibed embryo, biol rep 3 |
| GSM8588691 |
jmj13-m4, tassel stem, biol rep 1 |
| GSM8588692 |
jmj13-m4, tassel stem, biol rep 2 |
| GSM8588693 |
jmj13-m4, tassel stem, biol rep 3 |
| GSM8588694 |
myb40-m1, coleoptile tip, biol rep 1 |
| GSM8588695 |
myb40-m1, coleoptile tip, biol rep 2 |
| GSM8588696 |
myb40-m1, coleoptile tip, biol rep 3 |
| GSM8588697 |
myb40-m2, coleoptile tip, biol rep 1 |
| GSM8588698 |
myb40-m2, coleoptile tip, biol rep 2 |
| GSM8588699 |
myb40-m2, coleoptile tip, biol rep 3 |
| GSM8588700 |
mybr21-m1, imbibed embryo, biol rep 1 |
| GSM8588701 |
mybr21-m1, imbibed embryo, biol rep 2 |
| GSM8588702 |
mybr21-m1, imbibed embryo, biol rep 3 |
| GSM8588703 |
mybr32-m1, seedling leaf, biol rep 1 |
| GSM8588704 |
mybr32-m1, seedling leaf, biol rep 2 |
| GSM8588705 |
mybr32-m1, seedling leaf, biol rep 3 |
| GSM8588706 |
sbp20-m2, imbibed embryo, biol rep 1 |
| GSM8588707 |
sbp20-m2, imbibed embryo, biol rep 2 |
| GSM8588708 |
sbp20-m2, imbibed embryo, biol rep 3 |
| GSM8588709 |
sbp20-m3, imbibed embryo, biol rep 1 |
| GSM8588710 |
sbp20-m3, imbibed embryo, biol rep 2 |
| GSM8588711 |
sbp20-m3, imbibed embryo, biol rep 3 |
| GSM8588712 |
W22, coleoptile tip, biol rep 1 |
| GSM8588713 |
W22, coleoptile tip, biol rep 2 |
| GSM8588714 |
W22, coleoptile tip, biol rep 3 |
| GSM8588715 |
W22, coleoptile tip, biol rep 4 |
| GSM8588716 |
W22, imbibed embryo, biol rep 1 |
| GSM8588717 |
W22, imbibed embryo, biol rep 2 |
| GSM8588718 |
W22, imbibed embryo, biol rep 3 |
| GSM8588719 |
W22, imbibed embryo, biol rep 4 |
| GSM8588720 |
W22, seedling leaf, biol rep 1 |
| GSM8588721 |
W22, seedling leaf, biol rep 2 |
| GSM8588722 |
W22, seedling leaf, biol rep 3 |
| GSM8588723 |
W22, seedling leaf, biol rep 4 |
| GSM8588724 |
W22, tassel, biol rep 1 |
| GSM8588725 |
W22, tassel, biol rep 2 |
| GSM8588726 |
W22, tassel, biol rep 3 |
| GSM8588727 |
W22, tassel stem, biol rep 1 |
| GSM8588728 |
W22, tassel stem, biol rep 2 |
| GSM8588729 |
W22, tassel stem, biol rep 3 |
| GSM8588730 |
wrky2-m2, coleoptile tip, biol rep 1 |
| GSM8588731 |
wrky2-m2, coleoptile tip, biol rep 2 |
| GSM8588732 |
wrky2-m2, coleoptile tip, biol rep 3 |
| GSM8588733 |
wrky8-m1, imbibed embryo, biol rep 1 |
| GSM8588734 |
wrky8-m1, imbibed embryo, biol rep 2 |
| GSM8588735 |
wrky8-m1, imbibed embryo, biol rep 3 |
| GSM8588736 |
wrky8-m2, imbibed embryo, biol rep 1 |
| GSM8588737 |
wrky8-m2, imbibed embryo, biol rep 2 |
| GSM8588738 |
wrky8-m2, imbibed embryo, biol rep 3 |
| GSM8588739 |
wrky82-m1, imbibed embryo, biol rep 1 |
| GSM8588740 |
wrky82-m1, imbibed embryo, biol rep 2 |
| GSM8588741 |
wrky82-m1, imbibed embryo, biol rep 3 |
| GSM8588742 |
wrky87-m1, imbibed embryo, biol rep 1 |
| GSM8588743 |
wrky87-m1, imbibed embryo, biol rep 2 |
| GSM8588744 |
wrky87-m1, imbibed embryo, biol rep 3 |
| GSM8588745 |
wrky82-m2, imbibed embryo, biol rep 1 |
| GSM8588746 |
wrky82-m2, imbibed embryo, biol rep 2 |
| GSM8588747 |
wrky82-m2, imbibed embryo, biol rep 3 |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSE280139_grn-ms_gene-expression-data.tsv.gz |
81.8 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...