|
| Status |
Public on Jul 26, 2022 |
| Title |
WT_seedling_RNAseq_rep2 |
| 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 |
SAMN16784495 |
| SRA |
SRX9495630 |
