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Series GSE155368 Query DataSets for GSE155368
Status Public on Jan 26, 2021
Title Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [Small RNA-Seq]
Sample organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Third-party reanalysis
Summary Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements. This event is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilization. Hence, distinct epigenetic reprogramming events rewire transcription through major reorganization of the regulatory epigenome to guide the alternation of generations in flowering plants.
 
Overall design Re-analysis of published pollen small RNA-seq [SRR1567670, SRR1567672,SRR6208912,SRR12067243,SRR12067244,SRR12067245]
Adapter trimming was performed using cutadapt version 1.9.
Reads were aligned to the Arabidopsis genome (TAIR10) using the STAR version 2.7 requiring zero mismatches and ≤ 100 multiple end-to-end alignments
The resulting SAM files were used as input for readmapIO.py software (Schon et al., 2018) to reassign multimappers with a “rich-get-richer” algorithm.
The output bedFiles were sorted, condensed and normalized for total genome matching reads.
TAIR10 cDNA sequences (Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz)
*.bed: BED files of small RNAs
 
Contributor(s) Borg M, Papareddy RK
Citation(s) 33491647, 38816386
Submission date Jul 29, 2020
Last update date Jun 12, 2024
Contact name Michael Borg
E-mail(s) borgmichael@gmail.com
Organization name Gregor Mendel Institute
Lab Berger Lab
Street address Dr. Bohr-Gasse 3
City Vienna
ZIP/Postal code 1030
Country Austria
 
This SubSeries is part of SuperSeries:
GSE155369 Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis
Relations
Reanalysis of GSM1495677
Reanalysis of GSM1495679
Reanalysis of GSM2829912
Reanalysis of GSM4630744
Reanalysis of GSM4630745
Reanalysis of GSM4630746

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
GSE155368_Processed_data_description.xlsx 12.7 Kb (ftp)(http) XLSX
GSE155368_SRR1567670.norm.20-22.bed.gz 8.5 Mb (ftp)(http) BED
GSE155368_SRR1567670.norm.23-24.bed.gz 27.1 Mb (ftp)(http) BED
GSE155368_SRR1567672.norm.20-22.bed.gz 4.5 Mb (ftp)(http) BED
GSE155368_SRR1567672.norm.23-24.bed.gz 4.2 Mb (ftp)(http) BED
GSE155368_SRR6208912_GSM2829912_Col_FACS_pollen_Arabidopsis_thaliana_ncRNA-Seq.fastq.20.bam.bw 374.0 Kb (ftp)(http) BW
GSE155368_SRR6208912_GSM2829912_Col_FACS_pollen_Arabidopsis_thaliana_ncRNA-Seq.fastq.21.bam.bw 633.5 Kb (ftp)(http) BW
GSE155368_SRR6208912_GSM2829912_Col_FACS_pollen_Arabidopsis_thaliana_ncRNA-Seq.fastq.22.bam.bw 922.7 Kb (ftp)(http) BW
GSE155368_SRR6208912_GSM2829912_Col_FACS_pollen_Arabidopsis_thaliana_ncRNA-Seq.fastq.23.bam.bw 969.8 Kb (ftp)(http) BW
GSE155368_SRR6208912_GSM2829912_Col_FACS_pollen_Arabidopsis_thaliana_ncRNA-Seq.fastq.24.bam.bw 1.2 Mb (ftp)(http) BW
GSE155368_col0_leaf1.20.bam.bw 638.7 Kb (ftp)(http) BW
GSE155368_col0_leaf1.21.bam.bw 1.1 Mb (ftp)(http) BW
GSE155368_col0_leaf1.22.bam.bw 1.2 Mb (ftp)(http) BW
GSE155368_col0_leaf1.23.bam.bw 1.7 Mb (ftp)(http) BW
GSE155368_col0_leaf1.24.bam.bw 2.7 Mb (ftp)(http) BW
Processed data are available on Series record

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