GEO DataSets

(Submitter supplied) Single cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here, we use a second-generation single cell approach, where we zoom in on the root transcriptome by sorting cells with specific markers, to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: H5

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26208 GPL23157

12 Samples

Download data: H5

(Submitter supplied) Single cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here, we use a second-generation single cell approach, where we zoom in on the root transcriptome by sorting cells with specific markers, to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23157

6 Samples

Download data: CSV

(Submitter supplied) In addition to apical growth, plants undergo radial growth to increase girth, a particularly prominent feature in trees. During both apical and radial growth the phytohormones auxin and cytokinins form symmetries that govern further growth patterns. But whereas the gene regulatory networks interpreting the hormonal fields during apical growth are well established, such networks are not known for the radial growth. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL17133

25 Samples

Download data: CEL

(Submitter supplied) The mechanisms that allow cells in the plant meristem to coordinate tissue-wide maturation gradients with specialized cell networks are critical for indeterminate growth. Here, we combine long-term imaging, single-cell transcriptomics, genetic analysis, and network modeling to reconstruct the differentiation trajectory of the 20 protophloem cells in the Arabidopsis root. We found that lineage bifurcation and cellular specification are mediated near the stem cell niche by PEAR regulators. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

21 Samples

Download data: TXT

(Submitter supplied) The mechanisms that allow cells in the plant meristem to coordinate tissue-wide maturation gradients with specialized cell networks are critical for indeterminate growth. Here, we combine long-term imaging, single-cell transcriptomics, genetic analysis, and network modeling to reconstruct the differentiation trajectory of the 20 protophloem cells in the Arabidopsis root. We found that lineage bifurcation and cellular specification are mediated near the stem cell niche by PEAR regulators. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26208 GPL23157

30 Samples

Download data: TXT

(Submitter supplied) The mechanisms that allow cells in the plant meristem to coordinate tissue-wide maturation gradients with specialized cell networks are critical for indeterminate growth. Here, we combine long-term imaging, single-cell transcriptomics, genetic analysis, and network modeling to reconstruct the differentiation trajectory of the 20 protophloem cells in the Arabidopsis root. We found that lineage bifurcation and cellular specification are mediated near the stem cell niche by PEAR regulators. more...

Organism:

blank sample; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27787 GPL21785

1375 Samples

Download data: TXT

(Submitter supplied) Asymmetric cell division (ACD) and positional signals play critical roles in the tissue patterning during multicellular organ development. In the Arabidopsis root meristem, two major phloem cell types arise via ACDs of distinct origins: one for companion cells and the other for proto- and metaphloem sieve elements. The molecular mechanisms underlying each of these processes have been reported, however, how these two are coordinated has remained elusive. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9139

7 Samples

Download data: CEL

(Submitter supplied) We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To isolate phloem-specific genes in VISUAL, we performed GeneChip analysis after cell-sorting experiments with SEOR1pro::SEOR1-YFP.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL17416

6 Samples

Download data: CEL, CHP

(Submitter supplied) We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To compare gene expression profiles between WT and apl during vascular development, we performed GeneChip analysis using VISUAL.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL17416

6 Samples

Download data: CEL, CHP

(Submitter supplied) We profiled transcripts from sorted phloem cells of wild-type and apl mutants to identify the genes regulated by APL in phloem. We profiled transcripts from sorted phloem cells of wild-type and apl mutants to identify the genes regulated by APL in phloem.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) Comparison of the expression profiles of nac45-2 nac86 mutant with col WT, and comparison of the expression profiles of NAC45 extopical induction with non-induction.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

21 Samples

Download data: GPR

(Submitter supplied) A single cell RNA sequencing atlas of the Arabidopsis root distinguishes cells both by developmental fate and time, revealing defining expression features that depict a complex cascade of developmental progressions from stem cell through differentiation supported by mirroring waves of transcription factor expression. Methods: mRNA profiles of 6-day-old wild-type (WT) and shortroot-knockout Arabidopsis thaliana roots were generated by deep sequencing of single cell (all) and bulk RNA libraries (wild type only), in duplicate (bulk & wild-type single cell) and singlicate (shr-3), using Illumina NextSeq. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24270

7 Samples

Download data: CSV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17639 GPL13222

36 Samples

Download data: BW

(Submitter supplied) We report the application of laser capture microdissection (LCM) for high resolution transcriptome profiling of the second internode of the Arabidopsis thaliana inflorescence stem. In this series, we used LCM to determine and compare the transcriptome profiles of the phloem cap, the pith, and the remaining vascular bundle area.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: BW, CSV

(Submitter supplied) We report the Fluorescence Activated Nucleus Sorting (FANS)-based RNA sequencing for high resolution transcriptome profiling of the second internode of the Arabidopsis thaliana inflorescence stem. We compared GFP-positive nuclei and GFP negative nuclei from promoter reporter lines expressing Histone 4-GFP (NST3pro:H4-GFP, SMXL5pro:H4-GFP, APLpro:H4-GFP), and compared GFP positive nuclei from seven lines expressing Histone 4-GFP under the control of different tissue-specific promoters (NST3pro:H4-GFP, VND7pro:H4-GFP, PXYpro:H4-GFP, SMXL5pro:H4-GFP, APLpro:H4-GFP, SCRpro:H4-GFP, LTP1pro:H4-GFP).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

30 Samples

Download data: BW, CSV

(Submitter supplied) This sudy focuses on the identification of transcripts in the shoot phloem of the model plant Arabidopsis thaliana. Transcripts expressed in the phloem tissue (parenchyma cell, companion cell, sieve element) were excised by laser microdissection pressure catapulting (LMPC). These were compared with transcripts isolated from leaf phloem exudates by EDTA-chelation technique. Optimization of sample harvest resulted in RNA of high quality from both sources. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL, CHP

(Submitter supplied) Inflorescence architecture of Arabidopsis thaliana is regulated by ER-EPFL4/6 signaling module. To analyze the genes governed by this module, the transcriptional profiles of er-2 (allelic to er-106) mutant and epfl4 epfl6 double mutant were investigeted.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

9 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24163

6 Samples

Download data: MTX, TAB, TSV

(Submitter supplied) Leaves are asymmetric, with differential functionalization of abaxial and adaxial tissues. The bundle sheath (BS) surrounding the vasculature of the C3 crop barley is dorsoventrally differentiated into three domains: adaxial structural, lateral S-type, and abaxial L-type. S-type cells seem to transfer assimilates towards the phloem. Here we used single-cell RNA sequencing to investigate BS differentiation in C4 maize. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24163

4 Samples

Download data: TAB