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Sample GSM5941865 Query DataSets for GSM5941865
Status Public on Jul 26, 2022
Title H2B8 seedling PBS control RNA-seq replicate 2
Sample type SRA
 
Source name p35S::H2B.8-eGFP seedling
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype: p35S::H2B.8-eGFP
cell type: ten-day-old seedlings
Growth protocol Plants were grown under long day (16 hr light; 8 hr dark) conditions at 22 °C.
Extracted molecule total RNA
Extraction protocol The Plant RNeasy mini kit (QIAGEN) was used to extract RNA from 10-day-old seedlings.
Libraries were prepared with the Nugen Universal RNA-Seq library preparation kit (0364) and sequenced on the NextSeq 500 (Illumina) with 76 bp single end reads at the John Innes Centre, Norwich, UK.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description H2B8_drought_experiment_gene_expression_master.txt
Data processing ChIP-seq: Reads were mapped to TAIR10 using Bowtie2-2.3.4.1, retaining mononucleosomal fragments with using parameters -I 130 -X 200. Mapped reads were sorted and indexed using SAMtools-1.9.
ChIP-seq: Bigwig files were generated by normalising IP bam files to respective inputs with the bamCompare tool from deepTools-3.1.1. Bigwig files of enrichment were generated at single base resolution (w1) and at 50 bp intervals (w50).
ChIP-seq: To generate peaks, H2B.8 enrichment was calculated over 50 bp windows and those with > 0.5 log2(IP/input) were retained. Windows within 501 bp were merged using BEDtools-2.28.0. Regions were filtered by size, with those < 201 bp removed from analysis. H2B.8 enrichment was then calculated over the new regions, those with < 0.5 log2(IP/input) were discarded. The remaining regions were defined as H2B.8 peaks.
ChIP-seq: Overlaps with genes and TEs were determined using BEDtools-2.28.0; 50% of the feature was required to be overlapped by a peak to be defined as an overlap.
RNA-seq: Adapters were trimmed using TrimGalore-0.4.2.
RNA-seq: For differential expression analysis, reads were mapped to TAIR10 with TopHat-2.0.10. Kallisto-0.43.0 was used to obtain TPM (Transcripts Per Million) values. Pairwise statistical analysis was undertaken with Sleuth-0.30.0 in R-3.6.0. Differentially expressed genes and TEs were identified by log2 fold change of ≥ 2 and q < 0.05.
Hi-C: For Hi-C data assay, clean reads were mapped to TAIR10 genome using the HiC-Pro (version 2.11.1) pipeline. The bam files (bwt2merged.bam) generated by HiC-Pro containing mapping information were used as input files for Fan-C (version 0.9.8). The module ‘fanc auto’ was applied to generate 500 kb, 100 kb, 50 kb, 10 kb, 1kb contact matrix (hic files).
Assembly: TAIR10
Supplementary files format and content: ChIP-seq: Bigwig files generated with bamCompare in deepTools-3.1.1. Scores at w1 or w50 resolution represent log2(IP/input).
Supplementary files format and content: ChIP-seq: BED file of H2B.8 peaks in sperm and seedling.
Supplementary files format and content: ChIP-seq: BED file of H2B.8 peaks in sperm and seedling.
Supplementary files format and content: ChIP-seq: BED file of genes or TEs marked by H2B.8 in sperm and seedling.
Supplementary files format and content: RNA-seq: Matrix (.txt) file of WT and h2b.8 sperm cell replicate TPM values, fold change and q values for genes or TEs.
Supplementary files format and content: RNA-seq: Matrix (.txt) file of WT and p35S::H2B.8-eGFP seedling replicate TPM values, fold change and q values for genes or TEs.
Supplementary files format and content: RNA-seq: Matrix (.txt) file of drought treated and respective control WT and p35S::H2B.8-eGFP seedling replicate TPM values, fold change and q values for genes.
Supplementary files format and content: Hi-C: matrix and regions files of different resolution generated by Fan-C contain genomic contact and corresponding index information, respectively.
 
Submission date Mar 09, 2022
Last update date Jul 26, 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
 
Platform ID GPL19580
Series (1)
GSE161366 Histone H2B.8 compacts flowering plant sperm through chromatin phase separation
Relations
BioSample SAMN26543099
SRA SRX14434557

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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