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| Status |
Public on Feb 07, 2024 |
| Title |
Profiling trancriptome changes that affect vein specification in maize (Zea mays) tml (TOO MANY LATERALS) mutants |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The biochemistry of C4 photosynthesis relies on a specific suite of leaf functional properties, often referred to as Kranz anatomy, where there is increased vein density and the proportion of bundle sheath cells surrounding the veins compared to C3 photosynthesizing species. From a suite of putative Kranz anatomy regulators, TML was identified. Loss of function tml mutations lead to the development of large lateral veins in positions normally occupied by smaller intermediate veins in both C3 and C4 species tested. In order to elucidate the role of TML in vein patterning, we set out to profile transcriptional changes that happen in the leaf primordia upon tml knock-out in the C4 species Zea mays.
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| Overall design |
To investigate the effect of TML in vein patterning, we set out to profile transcriptional changes that happen in the leaf primordia, bulk plastochron 0 (P0) to plastochron 5 (P5) leaves including the shoot apical meristem (SAM) and the leaf sheath, of maize (Zea mays B104) upon tml1;tml2 knock-out. Loss of function alleles were generated by CRISPR/Cas9 mediated gene editing.
We then performed gene expression profiling analysis using leaf primordia samples (SAM, bulk P0 - P5) from 3 biological replicates of homozygous tml1;tml2 (segregating independently from the transgene) mutants and the respective segregating wildtypes.
Please note that the WTCHG_960488 and WTCHG_960489 represent two technical replicates of the same biological sample from different runs. The *_T1 data columns (in the processed data file) were generated from the WTCHG_960488* runs and *T2 data columns from the WTCHG_960489 runs.
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| Contributor(s) |
Zaidem M, Vlad D, Langdale J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Feb 06, 2024 |
| Last update date |
Feb 07, 2024 |
| Contact name |
Maricris Zaidem |
| E-mail(s) |
mzaidem@gmail.com, maricris.zaidem@biology.ox.ac.uk
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| Organization name |
University of Oxford
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| Department |
Department of Biology
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| Street address |
South Parks Rd
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| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX2 6GF |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL25410 |
Illumina NovaSeq 6000 (Zea mays) |
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| Samples (12)
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| GSM8066739 |
WT2, maize inbred line B104, segregating wild-type 2, sample A6 [WTCHG_960488_73595335] |
| GSM8066740 |
WT3, maize inbred line B104, segregating wild-type 3, sample B3 [WTCHG_960488_73635339] |
| GSM8066741 |
WT4, maize inbred line B104, segregating wild-type 4, sample H6 [WTCHG_960488_73705346] |
| GSM8066742 |
MT2, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 2, sample A2 [WTCHG_960488_73625338] |
| GSM8066743 |
MT3, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 3, sample D6 [WTCHG_960488_73675343] |
| GSM8066744 |
MT4, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 4, sample C3 [WTCHG_960488_73685344] |
| GSM8066745 |
WT2, maize inbred line B104, segregating wild-type 2, sample A6 [WTCHG_960489_73595335] |
| GSM8066746 |
WT3, maize inbred line B104, segregating wild-type 3, sample B3 [WTCHG_960489_73635339] |
| GSM8066747 |
WT4, maize inbred line B104, segregating wild-type 4, sample H6 [WTCHG_960489_73705346] |
| GSM8066748 |
MT2, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 2, sample A2 [WTCHG_960489_73625338] |
| GSM8066749 |
MT3, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 3, sample D6 [WTCHG_960489_73675343] |
| GSM8066750 |
MT4, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 4, sample C3 [WTCHG_960489_73685344] |
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| Relations |
| BioProject |
PRJNA1073974 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE255222_maize_tml_DESeq2_resSig05_esf_transcriptbased.txt.gz |
252.3 Kb |
(ftp)(http) |
TXT |
| GSE255222_maize_tml_genes_abundance_counts_length_matrix_updated.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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