How to read the data? Fluorescence-Activated Nucleus Sorting (FANS)
We generated seven lines expressing Histone 4-GFP under the control of different tissues-specific promoters and collected material from the second internode of the Arabidopsis inflorescence stem. GFP-positive nuclei were isolated by fluorescence-activated nucleus sorting (FANS). RNA was extracted from GFP positive nuclei, amplified using the Smart-seq2 method and then RNA-seq analysis was carried out. The expression pattern of each promoter is ...
- NST3pro : Fibers
- VND7pro: Xylem Vessels
- PXYpro: Cambium (Xylem side)
- SMXL5pro: Cambium (Phloem side)
- APLpro: Phloem
- SCRpro: Starch sheath
- LTP1pro: Epidermis.
Normalized read count values (by DESeq2) and p value of Likelyhood Ratio Test (LRT) results (by DESeq2) are shown. Please note that the null hypothesis to be rejected in the LRT test is that genes have similar expression among the seven different tissues.
How to read the data? Laser Capture Microdissection (LCM)
In addition to our FANS-based datasets, we collected the pith and the phloem cap by laser capture microdissection (LCM) using the rest of vascular bundle as a control. RNA was extracted from the cropped tissues and then submitted to RNA-seq analysis.
Normalized read count values (by DESeq2) and p value of Wald Test results (by DESeq2) are shown. In Wald test, gene expression in phloem cap or pith are compared with that of the control.
Contact
For further details, please see:
Shi, D., Jouannet, V., Agustí, J., Kaul, V., Levitsky, V., Sanchez, P., Mironova, V.V., Greb, T. Tissue-specific transcriptome profiling of the Arabidopsis thaliana inflorescence stem reveals local cellular signatures. The Plant Cell (2021)
doi 10.1093/plcell/koaa019
Comments, requests and questions are welcome to send to Dongbo Shi (COS Heidelberg) or Thomas Greb (COS Heidelberg). Please cite our paper when you use these datasets.
Developmental Physiology (Thomas Greb) group
Centre for Organismal Studies, Heidelberg, Germany
