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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Arabidopsis stem cell transcriptome

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 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.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Thomas Nussbaumer

PROVIDER: E-MTAB-5478 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Arabidopsis stem cell methylome

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 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.

2020-06-30 | E-MTAB-5479 | biostudies-arrayexpress

Transcriptome analysis of annotated coding genes and sORF under elevated CO2

Project description:There are seedling samples (high CO2 exposure of 0h, 2h, 6h, 12h, 1d, 3d, 7d, 14d) with duplicates in two chambers.

2015-12-31 | GSE49960 | GEO

Transcription profiling of mouse suprarenal aorta from ApoE knock-outs treated with angiotensin II or saline to study developing abdominal aortic aneurysm (AAA)

Project description:Transcriptional profiling of suprarenal aorta from ApoE-/- mice (12-14 weeks old, C57BL/6J background) treated by subcutaneous pump with angiotensin II or saline for 7d, 14d and 28d. Includes Ang II-treated samples at 7d found to have dissected aneurysms. Goal was to examine gene expression in developing AAA in this model over time. Experiment Overall Design: Two condition experiment, one suprarenal aorta per array. Saline vs. angiotensin II at 3 time points, with inclusion of 3 Ang II-treated dissected. Total 35 arrays: 6 saline 7d, 6 saline 14d, 5 saline 28d, 4 Ang II 7d, 5 Ang II 14d, 6 Ang II 28d, 3 Ang II-dissected 7d.

2009-10-09 | E-GEOD-17901 | biostudies-arrayexpress

Abdominal Aortic Aneurysm in the ApoE Knockout Mouse: Time Course of Control vs. Angiotensin II

2009-10-01 | GSE17901 | GEO

Transcriptome analysis of annotated coding genes and sORF under elevated CO2

Project description:There are seedling samples (high CO2 exposure of 0h, 2h, 6h, 12h, 1d, 3d, 7d, 14d) with duplicates in two chambers. Arabidopsis WT (Col-0) seeds were plated on Murashige and Skoog plates and placed at 4Â°C in darkness for at least 2 d to synchronize germination. Plants were grown at 22C under long-day conditions (16-h light and 8-h dark) in two atmospheric CO2 environments: ambient (CO2: 390 Î¼mol molâ??1) or elevated (CO2: 780 Î¼mol molâ??1). Plants were grown in ambient atmospheric CO2 concentration and then exposed to elevated CO2 for 0 h, 2 h, 6 h, 12 h, 1 d, 3 d, 7 d and 14 d. 14-d-old seedlings were sampled at the same time. Treatments for elevated CO2 were carried out two times using two different chambers. Duplicate samples were collected from each chamber experiment. Totally, four biologically replicates were prepared in each condition.

2015-12-31 | E-GEOD-49960 | biostudies-arrayexpress

Extensive, transient, and long-lasting gene regulation in a song-controlling brain area during testosterone-induced song development in adult female canaries

Project description:In this data set, we compared the expression data of song nuclei HVC dissected from adult female canaries (S. canaria) implanted with 7-mm SilasticTM tubes filled with testosterone for 6 periods (1h, 3h, 8h, 3d, 7d, and 14d) with control birds (implanted with empty tube) to identify testosterone effects on gene expression.

2019-12-31 | GSE118522 | GEO

Expression data from kidney transplantations in a Fisher-Lewis rat model: placebo and 13cisRA treatment

Project description:Most kidney allograft losses are caused by chronic allograft dysfunction (CAD). The aim of the study was to correlate changes in gene expression over time during the development of chronic damage in contrast to13cisRA Treated animal that demonstrated morphologically healthy kidneys by the end of teh study. Renal allografts were harvested from placebo and13cisRA Treatment groups for time points 0d, 7d, 14d and 56d (n=3-5) and examined for steady state mRNA expression using Affymetrix microarray RG-U34A. The effect of the13cisRA Treatment on dysregulated pathways was examined. In order to verify the microarray analysis, qPCR has been performed. Microarray data was used to obtain transcriptomic changes reflecting signaltransduction pathway dysregulation Progression of rejection was observed in untreated animals at timepoints 7d, 14d and 56d after transplantation that could be prevented by 13cisRA treatment

2012-01-07 | E-GEOD-17045 | biostudies-arrayexpress

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

Gene expression signatures following nerve injury in a rat model (0d-14d)

Project description:We used microarrays to distinguish the gene expression differences among different time points after injury. We generated L4-6 dorsal root ganglia (DRG) tissues and proximal sciatic nerve (SN) tissues (0.5cm) at 0d, 1d, 4d, 7d and 14d after sciatic nerve resection.

2013-01-01 | E-GEOD-30165 | biostudies-arrayexpress

QuantSeq/3' targeted seq supporting study Probing 3’UTRs as modular regulators of gene expression

Project description:The goal of the study is to analyze the function of 3'-UTR motifs in the non-native context. Several 3'-UTR motifs predicted to have stabilizing or destabilizing effects on mRNA were inserted into terminators controlling the expression of reporter mCherry gene in following contexts: pRps3-mCherry-tRps3, pPgk1-mCherry-tRps3, pTsa1-mCherry-tTsa. 3'-end sequencing was used to measure the levels of expression of reporter gene and distribution of poly(A) sites.

2022-04-09 | GSE200211 | GEO

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