|
| Status |
Public on Jul 24, 2017 |
| Title |
DNase-SEQ analysis of whole leaf and bundle sheath tissues in Zea mays, Sorghum bicolor, Setaria italica and Brachypodium distachyon. |
| Organisms |
Setaria italica; Sorghum bicolor; Zea mays; Brachypodium distachyon |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Photosynthesis supports life on Earth but the regulatory architecture associated with photosynthesis gene expression is poorly understood. Most crops use either C3 or C4 photosynthesis with the latter allowing significantly higher efficiencies as well as improved water and nitrogen use. Here we use DNAse-SEQ to define >1 million transcription factor binding sites in leaves of grasses that either operate C3 or C4 photosynthesis and that are consistent with significant differences in the modes of gene regulation between the kingdoms of life. Leaf samples were collected from seedlings to allow for comparison of regulatory interactions between species from the same (Zea mays and Sorghum bicolor) and different (Setaria italica) C4 lineages, as well as a C3 grass (Brachypodium distachyon) in order to investigate evolution of C4 photosynthetic gene expression. Additionally bundle sheath tissues were mechanically isolated from C4 species and analysed by DNAse-SEQ to identify DNA regulatory elements controlling cell-specific gene expression patterns.
|
| |
|
| Overall design |
Samples were collected from two tissue types (whole leaf and bundle sheath), with a minimum of two biological replicates per tissue resulting in a total of 17 samples.
|
| |
|
| Contributor(s) |
Burgess SJ, Reyna-Llorens I, Hibberd JM |
| Citation(s) |
31427470 |
|
Steven J. Burgess, Ivan Reyna-Llorens, Katja Jaeger, and Julian M. Hibberd. A transcription factor binding atlas for photosynthesis in cereals identifies a key role for coding sequence in the regulation of gene expression. bioRxiv 2017. doi: 10.1101/165787
|
| |
| Submission date |
Apr 04, 2017 |
| Last update date |
Jan 21, 2020 |
| Contact name |
Steven James Burgess |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Cambridge
|
| Department |
Plant Sciences
|
| Lab |
Molecular physiology
|
| Street address |
Department of Plant Sciences, Downing College
|
| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 3EA |
| Country |
United Kingdom |
| |
|
| Platforms (4)
|
| GPL20156 |
Illumina NextSeq 500 (Zea mays) |
| GPL20690 |
Illumina NextSeq 500 (Sorghum bicolor) |
| GPL23254 |
Illumina NextSeq 500 (Brachypodium distachyon) |
| GPL23255 |
Illumina NextSeq 500 (Setaria italica) |
|
| Samples (20)
|
|
| Relations |
| BioProject |
PRJNA381532 |
| SRA |
SRP102990 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE97369_DGF_Bd_WL.bed.gz |
3.1 Mb |
(ftp)(http) |
BED |
| GSE97369_DGF_DE_Sb_BS.bed.gz |
509.5 Kb |
(ftp)(http) |
BED |
| GSE97369_DGF_DE_Sb_WL.bed.gz |
592.5 Kb |
(ftp)(http) |
BED |
| GSE97369_DGF_DE_Si_BS.bed.gz |
640.5 Kb |
(ftp)(http) |
BED |
| GSE97369_DGF_DE_Si_WL.bed.gz |
403.5 Kb |
(ftp)(http) |
BED |
| GSE97369_DGF_DE_Zm_BS.bed.gz |
120.7 Kb |
(ftp)(http) |
BED |
| GSE97369_DGF_DE_Zm_WL.bed.gz |
87.5 Kb |
(ftp)(http) |
BED |
| GSE97369_DGF_Sb_BS.bed.gz |
2.0 Mb |
(ftp)(http) |
BED |
| GSE97369_DGF_Sb_WL.bed.gz |
2.3 Mb |
(ftp)(http) |
BED |
| GSE97369_DGF_Si_BS.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE97369_DGF_Si_WL.bed.gz |
2.0 Mb |
(ftp)(http) |
BED |
| GSE97369_DGF_Zm_BS.bed.gz |
2.4 Mb |
(ftp)(http) |
BED |
| GSE97369_DGF_Zm_WL.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE97369_DHS_Bd_WL.regionPeak.txt.gz |
872.3 Kb |
(ftp)(http) |
TXT |
| GSE97369_DHS_Sb_BS.regionPeak.txt.gz |
844.5 Kb |
(ftp)(http) |
TXT |
| GSE97369_DHS_Sb_WL.regionPeak.txt.gz |
999.5 Kb |
(ftp)(http) |
TXT |
| GSE97369_DHS_Si_BS.regionPeak.txt.gz |
934.6 Kb |
(ftp)(http) |
TXT |
| GSE97369_DHS_Si_WL.regionPeak.txt.gz |
968.7 Kb |
(ftp)(http) |
TXT |
| GSE97369_DHS_Zm_BS.regionPeak.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
| GSE97369_DHS_Zm_WL.regionPeak.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...