|
| Status |
Public on Jul 19, 2019 |
| Title |
WT_42DPA_Input_ Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA from 42 DPA WT pericarps
|
| Organism |
Solanum lycopersicum |
| Characteristics |
strain: Ailsa Craig
tissue: pericarps
developmental stage: 42 DPA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with hot-phenol reagent from 39 DPA and 42 DPA WT pericarps and 42 DPA Cnr mutant peicarps. mRNA was isolated from the total RNA and then fragmented, followed by immunoprecipitation with specific anti-m6A antibody.
For library construction, 50 ng of immunoprecipitated mRNAs or pre-immunoprecipitated mRNAs (input control) were used for library construction with NEBNext ultra RNA library prepare kit for illumina (NEB, E7530). High-throughput sequencing was performed on the illumina HiSeq X sequencer with a paired-end read length of 150 bp according to the standard protocols.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
grown in a standard greenhouse
WT_42DPA_Peaks_Rep3.tsv
|
| Data processing |
The quality of raw sequencing reads in m6A-seq was assessed using FastQC tool (Version 0.11.7). Adaptors and low-quality bases with a score < 20 located in the 3’-end were trimmed from all raw reads by Cutadapt software (version 1.16). After trimming, reads containing ambiguous nucleotides or with a length < 18 nt were filtered out by Trimmomatic (version 0.30). The remaining reads were analyzed by using FastQC tool once again to ensure sufficient quality assessment.
Reads alignment was performed with BWA (version 0.30) by using the tomato build_SL3.0 as a reference genome, and the ITAG3.2_release as a reference annotation (ftp://ftp.solgenomics.net/tomato_genome/).
Mapping Quality (MAPQ) of all aligned reads was concurrently calculated and only uniquely mapped reads with a MAPQ ≥ 13 were remained for the subsequent analysis for each sample (Dominissini et al., 2012).
MACS software (version 2.0.10) was used for the m6A peak identification in each anti-m6A immunoprecipitation sample with the corresponding input sample serving as a control. A stringent cutoff threshold for MACS-assigned false discovery rate (FDR) < 0.05 was used to obtain high-confidence peaks.
Genome_build: Tomato build_SL3.0
Supplementary_files_format_and_content: Tab-delimited tsv files include called peaks for each Sample
|
| |
|
| Submission date |
Jan 18, 2019 |
| Last update date |
Jul 19, 2019 |
| Contact name |
Leilei Zhou |
| E-mail(s) |
zhouleilei@ibcas.ac.cn
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Institute of botany
|
| Lab |
Key Laboratory of Plant Resources
|
| Street address |
No. 20 Nanxincun, Xiangshan, Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100093 |
| Country |
China |
| |
|
| Platform ID |
GPL24124 |
| Series (1) |
| GSE125306 |
RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 that is required for tomato fruit ripening |
|
| Relations |
| BioSample |
SAMN10769267 |
| SRA |
SRX5260795 |
