|
| Status |
Public on Feb 07, 2019 |
| Title |
smallRNAseq_DMS3-ZF_line2_x_NRPD-ZF1_T1_Figure7 |
| Sample type |
SRA |
| |
|
| Source name |
inflorescence
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: inflorescence
genotype: DMS3-ZF_x_NRPD1_ZF_in_Col-0
ecotype: Columbia
|
| Growth protocol |
All plants in this study were grown under long-day conditions (16h light/8h dark). Transgenic plants were obtained by agrobacterium-mediated floral dipping. T1 transgenic plants were selected on 1/2 MS medium + Glufosinate 50 μg/ml (Goldbio) or 1/2 MS medium + Hygromycin B 25 μg/ml (Invitrogen) in growth chambers under long day conditions and subsequently transferred to soil. Successive transgenic generations were germinated directly on soil.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from inflorescences was extracted using the Zymo Direct-zol Kit (ZYMO research).
For sRNA-seq libraries, 2ug total RNA was run in 15% UREA gels and small RNAs from 15 to 30bp were cut and precipitated. This RNA was used to prepare libraries using the Truseq small RNA kit (Illumina) following manufacturer’s instructions.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
small RNAseq of DMS3-ZF line2 x NRPD1-ZF T1 Figure7
|
| Data processing |
For sRNA-seq data analysis, raw reads were trimmed for Illumina adaptors using Cutadapt (v 1.9.1) and mapped to the TAIR10 reference genome using Bowtie (v1.1.0) (Langmead et al., 2009) allowing only one unique hit (-m 1) and zero mismatch. In order to define off-target sites with 24-nt siRNAs production, flanking 1kb of off-target region with NRPE1 recruitment were first divided into 100bp bins. Then 24-nt siRNAs count were calculated over those 100bp bins and DEseq2 (Love et al., 2014) was applied using 4 fold change and FDR less than 0.05 as cut off for DMS3-ZF vs ZF, NRPD1-ZF vs ZF and DMS3-ZF X NRPD1-ZF vs ZF.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Jan 07, 2019 |
| Last update date |
Feb 07, 2019 |
| Contact name |
Wanlu Liu |
| Organization name |
Zhejiang University
|
| Department |
Zhejiang University - University of Edinburgh Institute
|
| Lab |
Wanlu Liu
|
| Street address |
718 East Haizhou Rd.,
|
| City |
Haining |
| State/province |
Zhejiang |
| ZIP/Postal code |
314400 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE124546 |
Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis |
| GSE124749 |
Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [small RNA-seq] |
|
| Relations |
| BioSample |
SAMN10702039 |
| SRA |
SRX5213687 |
