|
| Status |
Public on Apr 13, 2021 |
| Title |
BM_CK_2 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Zea mays |
| Characteristics |
ecotype: B73xMo17
tissue: Seedlings
age: 14 days
|
| Growth protocol |
Plants were grown under normal condition with a photoperiod of 16 h light at 28°C and 8 h dark at 25°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Ambion life technologies) according to manufacturer’s protocol. Polysome-bound RNA was extracted as described in Zhang et al., 2017.
Libraries of RNA-seq, m6A-seq, and polysome profiling for F1 hybrid were constructed using the NEBNext Ultra II RNA Library Prep Kit (E7770S, NEB) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
PolyA RNA
|
| Data processing |
Base calling was performed following the standard Illumina protocol.
Raw paired-end reads of m6A-Seq, RNA-Seq and polysome profiling 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 and F1 hybrid B73×Mo17 were mapped to the maize B73 reference genome (AGPv4.38) and clean reads from Mo17 were mapped to the maize Mo17 pseudogenome constructed by substituting maize B73 reference genome (AGPv4.38) with single nucleotide polymorphisms from Mo17 (CAU-1.0) using Hisat2 (v2.1.0).
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 for each sample.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of genes for each sample.
|
| |
|
| Submission date |
Aug 09, 2020 |
| Last update date |
Apr 13, 2021 |
| Contact name |
Yan He |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE155947 |
Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize |
|
| Relations |
| BioSample |
SAMN15770384 |
| SRA |
SRX8913961 |
