|
| Status |
Public on Sep 16, 2019 |
| Title |
B_CK_2 |
| Sample type |
SRA |
| |
|
| Source name |
B73_RNA-seq
|
| Organism |
Zea mays |
| Characteristics |
ecotype: B73
developmental stage: 14-day-old
tissue: seedings
library sta: RNA-seq
|
| Growth protocol |
Plants were grown under normal condition with a photoperiod of 16 h light at 28°C and 8h dark at 25°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Trozol reagent (Ambion life technologies) according to manufacturer’s protocol. Polysome-bound RNA was extracted as described in Zhang et al., 2017.
m6A-seq ,RNA-seq and polysome profiling libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S, NEB) following manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Base calling was performed following the standard Illumina protocol.
Raw paired-end reads of m6A-Seq and input RNA-Seq were filtered and adapter sequences were trimmed out by Trimmomatic (v0.35) with parameters ILLUMINACLIP TruSeq3-PE-2.fa MINLEN 30.
Cleaned reads from B73 samples were aligned to maize B73 reference genome (AGPv4.38) and cleaned reads from Mo17 samples were mapped to maize Mo17 reference genome (CAU-1.0) using Hisat2 with parameters -5 1 -3 1 --dta.
Reads matching to less than five places were retained for further analysis.
m6A peaks were identified using the MACS2 peak calling algorithm with the input as background and the parameter of effective genome size was adjusted to the transcriptome size (417272442) and q value was set to 0.01.
Genome_build: Zea mays B73 RefGen_v4, Zm-Mo17-REFERENCE-CAU-1.0
Supplementary_files_format_and_content: Tab-delimited text files include m6A peaks locus or FPKM values of genes for each Sample.
|
| |
|
| Submission date |
Jan 02, 2019 |
| Last update date |
Sep 17, 2019 |
| Contact name |
Yan He |
| E-mail(s) |
yh352@cau.edu.cn
|
| Organization name |
China Agricultural University
|
| Department |
Plant Genetics and Breeding
|
| Lab |
He Lab
|
| Street address |
2 Yuanmingyuan West Road
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL25842 |
| Series (1) |
| GSE124543 |
Natural variation in RNA m6A methylation and its relationship with translational status. |
|
| Relations |
| BioSample |
SAMN10678459 |
| SRA |
SRX5192963 |
