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Sample GSM4905395 Query DataSets for GSM4905395
Status Public on Jul 26, 2022
Title WT_seedling_RNAseq_rep1
Sample type SRA
 
Source name WT seedling
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype: WT
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. RNA was converted to cDNA by RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific).
Libraries were prepared with the Nugen Universal RNA-Seq library preparation kit (0364) and sequenced on the NextSeq 500 (Illumina) with 2 × 38 bp paired 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 Seedling_genes_RNAseq_TPM_foldchange_Pval_matrix.txt
Seedling_TEs_RNAseq_TPM_foldchange_Pval_matrix.txt
Data processing 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 fold change of ≥ 2 and p < 0.05.
RNA-seq: For comparisons of expression between cell types, reads were mapped using HISAT2-2.1.0. Cufflinks-2.2.1 and Ballgown-2.16.0 in R-3.6.0 were used to generate FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: Matrix (.txt) file of WT and h2b.8 sperm cell replicate TPM values, fold change and P values for genes or TEs.
Supplementary_files_format_and_content: RNA-seq: Matrix (.txt) file of WT and 35Sp::H2B.8-eGFP seedling replicate TPM values, fold change and P values for genes or TEs.
 
Submission date Nov 12, 2020
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 SAMN16784496
SRA SRX9495629

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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