Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq after FANS of WOX2 marked cells after 3 days of somatic embryogenesis induction in Arabidopsis.

ABSTRACT: The pWOX2::H2B-GFP Arabidopsis line was used to induce somatic embryogenesis following the SE induction protocol described by Gaj (2001). After three days of somatic embryogenesis induction, nuclei were isolated from the upper part of the explants (immature zygotic embryos) and subjected to fluorescence-activated nuclear sorting (FANS). During sorting, two nuclear fractions were collected: GFP-positive and GFP-negative nuclei. RNA was extracted, converted to cDNA and sequenced on an illumina NovaSeq SP SR100.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Anna Wójcik

PROVIDER: E-MTAB-16183 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Cyclamen persicum zygotic embryo, callus and somatic embryo

Project description:The goal of the experiment was to investigate impact of the apoplast on somatic embryogenesis in Cyclamen persicum

2010-04-20 | E-TABM-837 | biostudies-arrayexpress

Transcriptome profiling of inflorescence stem tissues from Arabidopsis thaliana series 1

Project description: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).

2020-02-10 | GSE142032 | GEO

Subsets of visceral adipose tissue nuclei with discrete levels of 5-hydroxymethylcytosine

Project description:We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We developed fluorescence nuclear cytometry (FNC) and fluorescence activated nuclear sorting (FANS) of cellular nuclei from Sus scrofa visceral adipose tissue (SsVAT) using the levels of the pan-adipocyte protein, peroxisome proliferator-activated receptor gamma-2 (PPARg2) to distinguish PPARg2-Positive nuclei from PPARg2-Neg (negative) leukocyte, endothelial, and adipocyte progenitor cell nuclei. PPARg2-Postive VAT nuclei showed 2- to 50-fold higher levels of transcripts encoding most of the chromatin-remodeling factors assayed regulating the methylation of histones and DNA cytosine (e.g., DNMT1, DNMT3A, TET2, TET3, KMT2C, SETDB1, PAXP1, ARID1A, KMT2C, JMJD6, CARM1/PRMT4, PRMT5). PPARg2-Positive nuclei have a large decondensed chromatin structure. TAB-seq demonstrated 5Â´-hydroxymethylcytosine (5hmC) levels were remarkably dynamic in the gene body of PPARg2-Positive nuclei, dropping 3.8-fold from the highest quintile of expressed genes to the lowest. Sus scrofa VAT (SsVAT) nuclei were isolated from SsVAT. SsVAT nuclei were stained with PPARg2 and sorted with fluorescence activated nuclear sorting (FANS) into PPARg2-High, PPARg2-Med (Medium), PPARg2-Low, and PPARg2-Neg (Negative) four populations.TAB-seq data on 5-hydroxymehtylcytosine (Yu, M. et al. 2012. Cell 149, 1368-1380) was collected from genomic DNA isolated from PPARg2-High, PPARg2-Med+Low (pooled PPARg2-Med and PPARg2-Low), and PPARg2-Neg SsVAT nuclei.

2016-07-20 | E-GEOD-73684 | biostudies-arrayexpress

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

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

Potential link between biotic defense activation and recalcitrance to induction of somatic embryogenesis in shoot primordia from adult trees of white spruce (Picea glauca)

Project description:The goal is to examine the molecular aspects underpinning somatic embryogenesis (SE) within shoot tissues of adult white spruce trees by conducting transcriptome-wide expression profiling of shoot explants taken from responsive and nonresponsive genotypes. One-color analysis of vegetative buds in somatic embryogenesis responsive and nonresponsive genotypes, before and after 7 days of SE induction. There are 5 biological replicates for each of the 4 combinations of genotype/time of induction for a total of 20 slides. Each replicate is comprised of a pool of 6 buds.

2013-10-17 | E-GEOD-46977 | biostudies-arrayexpress

Genome-wide profiling at single-nucleotide resolution of brain cell types in schizophrenia [WGBS]

Project description:We carried out cell-type specific whole genome bisulfite sequencing from BA46 that underwent fluorescence-activated nuclei sorting (FANS).

2019-06-25 | GSE107729 | GEO

Proteome of Douglas-fir: a resource for genomic research

Project description:First Douglas fir proteomes by nLC-MS/MS from 12 different organs : root, stem, xylem, needle, bud, female and male flowers, immature and mature seed, immature and mature somatic embryos and callus.

2023-10-24 | PXD037815 | Pride

Whole genome bisulfite sequencing from primate brains (orthologous region to human BA46)

Project description:We carried out cell-type specific whole genome bisulfite sequencing from primate brains (orthologous region to human BA46) that underwent fluorescence-activated nuclei sorting (FANS).

2021-02-01 | GSE151768 | GEO

FANS-assisted ATAC-Seq to identify developmentally active endothelial enhancers [ATAC-seq]

Project description:Fluorescence-Activated Nuclei Sorting (FANS)-assisted Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) This work sought to identify endothelial-specific enhancer elements by applying ATAC-Seq to nuclei isolated from Tg(fli1a:egfp) transgenic zebrafish embryos.

2017-06-08 | GSE97255 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data