NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE54560 Query DataSets for GSE54560
Status Public on Feb 03, 2015
Title Genome-wide profiling of H3K4me3, H3K27me3 H3K27me1 and 5mC enrichment and mRNA levels in young leaves of Arabis alpina
Organism Arabis alpina
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Chromatin, DNA and RNA were extracted from young A. alpina Pajares primary stem leaves. Chromatin and DNA methylation immunoprecipitation experiments were performed using commercially available antibodies and analyzed by Illumina sequencing (ChIP-seq and MeDIP-seq). Transcriptome data were generated by RNA-seq.
 
Overall design ChIP-seq analysis of H3K4me3, H3K27me3 and H3K27me1 enrichment profiles and MeDIP-seq analysis of 5mC enrichment profiles in 2 biological replicates. RNA-seq analysis of mRNA levels in 1 biological replicate.
 
Contributor(s) Chica C, Szarzynska B, Roudier F, Colot V
Citation Eva-Maria Willing, Vimal Rawat, Terezie Mandáková, Florian Maumus, Geo Velikkakam James, Karl J.V. Nordström, Claude Becker, Norman Warthmann, Claudia Chica, Bogna Szarzynska, Matthias Zytnicki, Maria C. Albani, Christiane Kiefer, Sara Bergonzi, Loren Castaings, Julieta L. Mateos, Markus C. Berns, Nora Bujdoso, Thomas Piofczyk, Laura de Lorenzo, Cristina Barrero-Sicilia, Isabel Mateos, Mathieu Piednoël, Jörg Hagmann, Romy Chen-Min-Tao, Raquel Iglesias-Fernández, Stephan C. Schuster, Carlos Alonso-Blanco, François Roudier, Pilar Carbonero, Javier Paz-Ares, Seth J. Davis, Ales Pecinka, Hadi Quesneville, Vincent Colot, Martin A. Lysak, Detlef Weigel, George Coupland & Korbinian Schneeberger. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nat Plants 2015;1:23. doi:10.1038/nplants.2014.23
Submission date Jan 30, 2014
Last update date May 15, 2019
Contact name François ROUDIER
E-mail(s) francois.roudier@ens-lyon.fr
Organization name Ecole Normale Supérieure de Lyon
Department Biologie
Lab RDP
Street address 46 Allée d'Italie
City Lyon
ZIP/Postal code 69364
Country France
 
Platforms (1)
GPL18238 Illumina Genome Analyzer IIx (Arabis alpina)
Samples (12)
GSM1318862 Aa_H3K4me3_rep1
GSM1318863 Aa_H3K4me3_rep2
GSM1318864 Aa_H3K27me3_rep1
This SubSeries is part of SuperSeries:
GSE54728 Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
Relations
BioProject PRJNA237036
SRA SRP036074

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE54560_Aa_5mC_coVcomp.bedGraph.gz 267.2 Mb (ftp)(http) BEDGRAPH
GSE54560_Aa_5mC_domains.bed.gz 507.4 Kb (ftp)(http) BED
GSE54560_Aa_H3K27me1_coVcomp.bedGraph.gz 205.7 Mb (ftp)(http) BEDGRAPH
GSE54560_Aa_H3K27me1_domains.bed.gz 449.6 Kb (ftp)(http) BED
GSE54560_Aa_H3K27me3_coVcomp.bedGraph.gz 378.4 Mb (ftp)(http) BEDGRAPH
GSE54560_Aa_H3K27me3_domains.bed.gz 193.0 Kb (ftp)(http) BED
GSE54560_Aa_H3K4me3_coVcomp.bedGraph.gz 301.9 Mb (ftp)(http) BEDGRAPH
GSE54560_Aa_H3K4me3_domains.bed.gz 321.7 Kb (ftp)(http) BED
GSE54560_Aa_INPUT-5mC_coVcomp.bedGraph.gz 365.1 Mb (ftp)(http) BEDGRAPH
GSE54560_Aa_INPUT_coVcomp.bedGraph.gz 236.8 Mb (ftp)(http) BEDGRAPH
GSE54560_Aa_mRNA_covexonsByGene.txt.gz 365.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap