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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Arabidopsis stem cell methylome

ABSTRACT: Arabidopsis shoot apical meristem (SAM) stem cells were labelled with a CLV3:H2B-mCherry reporter. This reporter allowed fluorescence activated nuclear sorting (FANS) of nuclei of stem cells at 2 different developmental stages: 14d old seedling and 5 weeks old seedlings. DNA was extracted, bisulfite-converted and sequenced on an illumina HiSeq 2500 platform.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Thomas Nussbaumer

PROVIDER: E-MTAB-5479 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Arabidopsis stem cell transcriptome

Project description:Arabidopsis shoot apical meristem (SAM) stem cells were labelled with a CLV3:H2B-mCherry reporter. This reporter allowed fluorescence activated nuclear sorting (FANS) of nuclei of stem cells at 4 different developmental stages: Embryo (heart-torpedo), 7d old seedling, 14d old seedling and 5 weeks old seedlings. RNA was extracted, converted to cDNA and sequenced on an illumina HiSeq 2500 platform.

2018-12-30 | E-MTAB-5478 | biostudies-arrayexpress

Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways

Project description:The shoot apical meristem (SAM) of angiosperm plants is a highly organized minute structure that gives rise to all above-ground organs. The SAM is divided into three different functional domains. The central zone (CZ) at the SAM tip harbors the self-renewing pluripotent stem cells and the organizing center, providing daughter cells that are continuously displaced into the interior rib zone (RZ) or to the surrounding peripheral zone (PZ), from which organ primordia are initiated. Despite the constant flow of cells from the CZ into the RZ or PZ, and cell recruitment for primordium formation, a stable balance is maintained between the distinct cell populations in the SAM. Here we combined an in depth phenotypic analysis with a comparative RNA-Seq approach to characterize meristems from selected combinations ofÂ clavata3 (clv3),Â jabba-1DÂ (jba1D) andÂ erecta (er) mutants. We demonstrate that CLV3 restricts meristem expansion along the apical basal axis, while class III HD-ZIP and ER pathways restrict meristem expansion laterally, but in distinct and possibly perpendicular orientations. OurÂ k-means analysis reveals thatÂ clv3,Â jba-1D/+ andÂ erÂ lead to meristem enlargement by affecting different aspects of meristem function, e.g., thatÂ clv3Â displays increase in stem cell population, whereasÂ jba-1D/+Â er exhibits increase in mitotic activity and in meristematic cell population. We demonstrate that thecombination of genetic and mRNA-Seq comparative approach provides a precise and sensitive method to identify cell type specific transcriptomes in a small structure such as the SAM. Ten samples enriched in shoot apical meristem tissue were analyzed, corresponding to 5 different genotypes (Col-0, clv3-2, jba-1D/+, jba-1D/+ er-20, and jba-1D/+ er-20 clv3-2) at two different developmental stages (8-day-old seedlings and 15-day-old seedlings).

2016-04-02 | E-GEOD-79839 | biostudies-arrayexpress

Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways

Project description:The shoot apical meristem (SAM) of angiosperm plants is a highly organized minute structure that gives rise to all above-ground organs. The SAM is divided into three different functional domains. The central zone (CZ) at the SAM tip harbors the self-renewing pluripotent stem cells and the organizing center, providing daughter cells that are continuously displaced into the interior rib zone (RZ) or to the surrounding peripheral zone (PZ), from which organ primordia are initiated. Despite the constant flow of cells from the CZ into the RZ or PZ, and cell recruitment for primordium formation, a stable balance is maintained between the distinct cell populations in the SAM. Here we combined an in depth phenotypic analysis with a comparative RNA-Seq approach to characterize meristems from selected combinations of clavata3 (clv3), jabba-1D (jba1D) and erecta (er) mutants. We demonstrate that CLV3 restricts meristem expansion along the apical basal axis, while class III HD-ZIP and ER pathways restrict meristem expansion laterally, but in distinct and possibly perpendicular orientations. Our k-means analysis reveals that clv3, jba-1D/+ and er lead to meristem enlargement by affecting different aspects of meristem function, e.g., that clv3 displays increase in stem cell population, whereas jba-1D/+ er exhibits increase in mitotic activity and in meristematic cell population. We demonstrate that thecombination of genetic and mRNA-Seq comparative approach provides a precise and sensitive method to identify cell type specific transcriptomes in a small structure such as the SAM.

2016-04-02 | GSE79839 | GEO

Analysis of the mp clv3 transcriptome profile in Arabidopsis

Project description:Due to the major limitation of small set of stem cells located in the Shoot Apical Meristem (SAM), it is difficult to perform the whole genome analysis specific for those stem cells. Here, we generated the mp clv3 double mutant with a larger Shoot Apical Meristem,in which shoot stem cells were drastically enriched while the differentiation of stem cells was blocked. Then we performed the mRNA profiling on wild type and mp clv3 double mutant. And this could offer an ideal genetic material to highly increase the resolution of plant shoot stem cell profiling, also to further explore the mechanism of plant stem-cell regulation.

2021-06-24 | GSE77169 | GEO

RNA-seq of Arabidopsis 14 day-old seedlings expressing either mCherry-RAX1-GR or mCherry-GR with 4h mock vs. dexamethasone treatment

Project description:In order to identify relevant target genes of RAX1 (AT5G23000) involved in meristem initiation in Arabidopsis we generated dexamethasone inducible lines expressing either a mCherry-RAX1-GR or a mCherry-GR (mock construct) fusion protein. We analysed differential gene regulation after 4 hours of dexamethasone or mock treatment in 14 day-old seedlings. Paired-end sequencing was performed using 3 biological replicate for each genotype and differentially expressed genes were identified for the interaction of genotype and treatment.

2019-07-01 | E-MTAB-7050 | biostudies-arrayexpress

scRNAseq of Cyp11a1-expressing cells from mouse melanoma model derived tumors

Project description:Tumours induce de novo steroidogenesis in immune cells. We wanted to define the gene expression identity of intratumoural steroidogenic immune cells and compare them with the transcriptome with non-steroidogenic cells. Cyp11a1 expression is a faithful biomarker of de novo steroidogenesis (i.e. Cyp11a1+ cells are steroidogenic and Cyp11a1- cells are non-steroidogenic). We inoculated B16-F10 tumor in Cyp11a1-mCherry reporter mice, enriched and purified intratumoral Cyp11a1-mCherry+ and Cyp11a1-mCherry- cells by cell sorting into 96-well plates [with a ratio of 79:15 (mCherry+ : mCherry-) cells per plate] and performed scRNA-seq using SMART-Seq2 platform.

2020-05-27 | E-MTAB-8509 | biostudies-arrayexpress

Mouse Pancreatic Islet Maturation Time Series

Project description:Beta cells are the sole source of insulin in our body, yet we do not understand how they mature into fully functional, glucose-responsive beta cells. We generated transcriptomes of FACS-purified beta cells using the Ins1-H2b-mCherry reporter line (Jax # 028589) at different peri- and postnatal maturation stages. This enables a systematic comparison across thousands of genes as beta cells mature.

2017-04-04 | GSE88779 | GEO

mRNA-seq analysis of Caenorhabditis elegans daf-18(ok480) and WT starved L1 larvae shortly after hatching

Project description:Whole L1 larvae were collected from GC1459 [naSi2 [pGC550 (mex-5p::mCherry::H2B::nos-2 3'UTR +unc-119(+))] II; unc-119(ed3) III ?; daf-18(ok480) IV] and GC1171 [naSi2 [pGC550 (mex-5p::mCherry::H2B::nos-2 3'UTR +unc-119(+))] II; unc-119(ed3) III] strains up to two hours after hatching without food.

2021-06-21 | GSE151299 | GEO

RNA-Seq analysis after overexpression of AtmiR165a in Arabidopsis Shoot Apical Meristem in clv3 mutant background

Project description:Results from experiments done on knock-down of adaxial class III HD ZIP genes, using overexpression of miR165a, in clv3 shoot meristem show that Class III HD-ZIP genes act generally to repress the formation of new growth axes where they are expressed. This study explored the genes directly regualted by miRNAs as well as indirectly regulated by class III HD-ZIPs.

2025-08-31 | GSE212407 | GEO

Cas13d experimental viral genome-wide screen identifies regions of RNA vulnerability in SARScov2

Project description:We performed an experimental Cas13d-SARScov2 genome-wide screen to identify gRNAs that would allow Cas13d to degrade the viral RNA. We built mCherry reporter plasmids that express mCherry with a 3kb 3'UTR deriving from the SARScov2 genome. In total we designed 11 reporters covering the entire plus strand of the viral genome and 11 other reporters covering the entire minus strand. Each of the 22 mCherry reporter plasmids carries a U6 expression cassette containing a Cas13d gRNA that targets the 3'UTR of the mCherry reporter. Each reporter is represented by a pool of reporters each containing a different gRNA that targets mCherry 3'UTR for a total average of ~300 gRNA per 3'UTR. The entire pool of 22 reporters, each with a pool of ~300 different gRNAs constitutes a comprehensive set ~6,500 reporters (~ 6,500 different gRNAs) that allowed us to interrogate the entire SARScov2 plus and minus strand viral RNA for regions of vulnerability and targetability. In order to specifically interrogate Cas13d activity an remove the biases that would be introduced in the reporter expression by the presence of a large 3kb 3'UTR we used a case (presence of Cas13d) control (absence of Cas13d) design. Briefly, the ~6,500 reporters were lentiviral transduced in RKO cells, the cells were split in 2 populations, 1 population was transduced with Cas13d and the other serving as control did not. The population expressing Cas13d was FACS sorted in low mCherry (efficient gRNAs) and high mCherry (un-efficient gRNAs) in 2 biological replicates and the genomic DNA of these populations was extracted, gRNAs were PCR amplified and sequenced. For the population that did not express Cas13d, a low mCherry, one high mCherry and unsorted population were sequenced as control libraries.

2023-10-29 | E-MTAB-11111 | biostudies-arrayexpress

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