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Series GSE161366 Query DataSets for GSE161366
Status Public on Jul 26, 2022
Title Histone H2B.8 compacts flowering plant sperm through chromatin phase separation
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
Summary We characterised a sperm-expressed histone variant, H2B.8 in Arabidopsis by performing ChIP-seq, RNA-seq, and Hi-C. The data show that H2B.8 is exclusively deposited to unexpressed euchromatin and that gene expression is not significantly affected either by h2b.8 mutation in sperm or overexpression in soma. The deposition of H2B.8increases the contact probability of short range intrachromosomal interactions and contacts between pericentomeric regions and chromosome arms of different chromosomes.
 
Overall design ChIP-seq profiles of H2B.8 in sperm and ectopic H2B.8 in seedlings. Native ChIP-seq of H2B.8p::H2B.8-eGFP pollen and 35Sp::H2B.8-eGFP seedlings was used with GFP-Trap beads for immunoprecipitation. The ChIP-seq data includes two replicates of IP and respective inputs each. RNA-seq data comparing WT and h2b.8 mutant sperm cells and WT and H2B.8 ectopic expression (35Sp::H2B.8-eGFP) seedlings. The data includes two replicates of sperm cells and three replicates of seedlings for each. Hi-C data for WT and H2B.8 ectopic expression (35Sp::H2B.8-eGFP) seedlings.
 
Contributor(s) Buttress T, He S, Wang L, Zhou S, Saalbach G, Vickers M, Li G, Li P, Feng X
Citation(s) 36323776
Submission date Nov 12, 2020
Last update date Nov 18, 2022
Contact name Xiaoqi Feng
E-mail(s) xiaoqi.feng@jic.ac.uk
Organization name John Innes Centre
Department Cell and Developmental Biology
Lab Xiaoqi Feng
Street address Norwich Research Park
City Norwich
State/province Norfolk
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platforms (2)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL23157 HiSeq X Ten (Arabidopsis thaliana)
Samples (48)
GSM4905383 H2B8_sperm_IP_rep1
GSM4905384 H2B8_sperm_input_rep1
GSM4905385 H2B8_sperm_IP_rep2
Relations
BioProject PRJNA677963
SRA SRP292364

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
GSE161366_H2B8_drought_experiment_gene_expression_master.txt.gz 3.0 Mb (ftp)(http) TXT
GSE161366_H2B8_seedling_control_both_reps_w50.bw 18.2 Mb (ftp)(http) BW
GSE161366_H2B8_seedling_drought_both_reps_w50.bw 18.0 Mb (ftp)(http) BW
GSE161366_H2B8_seedling_peaks.bed.gz 224.2 Kb (ftp)(http) BED
GSE161366_H2B8_sperm_peaks.bed.gz 306.1 Kb (ftp)(http) BED
GSE161366_RAW.tar 6.5 Gb (http)(custom) TAR (of BW, MATRIX, TXT)
GSE161366_Seedling_TEs_RNAseq_TPM_foldchange_Pval_matrix.txt.gz 340.0 Kb (ftp)(http) TXT
GSE161366_Seedling_genes_RNAseq_TPM_foldchange_Pval_matrix.txt.gz 1.0 Mb (ftp)(http) TXT
GSE161366_Sperm_cell_TEs_RNAseq_TPM_foldchange_Pval_matrix.txt.gz 127.6 Kb (ftp)(http) TXT
GSE161366_Sperm_cell_genes_RNAseq_TPM_foldchange_Pval_matrix.txt.gz 599.4 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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