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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 03, 2015 |
| Title |
Genome-wide profiling of H3K4me3, H3K27me3 H3K27me1 and 5mC enrichment and mRNA levels in young leaves of Arabidopsis lyrata |
| Organism |
Arabidopsis lyrata |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
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| 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.
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| 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.
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| 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
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| Submission date |
Feb 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
François ROUDIER |
| E-mail(s) |
francois.roudier@ens-lyon.fr
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| Organization name |
Ecole Normale Supérieure de Lyon
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| Department |
Biologie
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| Lab |
RDP
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| Street address |
46 Allée d'Italie
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| City |
Lyon |
| ZIP/Postal code |
69364 |
| Country |
France |
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| Platforms (1) |
| GPL16940 |
Illumina Genome Analyzer IIx (Arabidopsis lyrata) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE54728 |
Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation |
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| Relations |
| BioProject |
PRJNA237509 |
| SRA |
SRP036730 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE54727_Al_5mC_coVcomp.bedGraph.gz |
227.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE54727_Al_5mC_domains.bed.gz |
298.1 Kb |
(ftp)(http) |
BED |
| GSE54727_Al_H3K27me1_coVcomp.bedGraph.gz |
152.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE54727_Al_H3K27me1_domains.bed.gz |
150.2 Kb |
(ftp)(http) |
BED |
| GSE54727_Al_H3K27me3_coVcomp.bedGraph.gz |
327.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE54727_Al_H3K27me3_domains.bed.gz |
167.2 Kb |
(ftp)(http) |
BED |
| GSE54727_Al_H3K4me3_coVcomp.bedGraph.gz |
252.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE54727_Al_H3K4me3_domains.bed.gz |
198.1 Kb |
(ftp)(http) |
BED |
| GSE54727_Al_INPUT-5mC_coVcomp.bedGraph.gz |
299.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE54727_Al_INPUT_coVcomp.bedGraph.gz |
223.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE54727_Al_mRNA_covexonsByGene.txt.gz |
349.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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