|
| Status |
Public on May 16, 2020 |
| Title |
dek53-ref-2 |
| Sample type |
SRA |
| |
|
| Source name |
kernel
|
| Organism |
Zea mays |
| Characteristics |
tissue: kernel
age: 15 DAP
genotype: dek53-ref
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent (Tiangen), followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
Maize 35 mitochondrial genes were PCR-amplified from dek53-ref and WT-ref, dek53-mu1 and WT-mu1 kernel cDNA.RT-PCR amplicons obtained from each template were mixed in an equimolar ratio and sheared by sonication. Sequencing libraries were generated using a NEB Next Ultra DNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
fastq reads were aligned using bowtie2 (v2.3.5) with default setting (customized genome build mtcds.fa)
SAM file were converted and sorted by samtools (v1.9) to BAM format
allele frequencies were count by bam-readcount (v0.8.0) with -q 30 -b 30 -d 10000000
Genome_build: mtcds.fa (supplemental data)
Supplementary_files_format_and_content: Tab-delimited text files include allele frequencies for each nucleotide (supplemental data)
|
| |
|
| Submission date |
May 15, 2020 |
| Last update date |
Jul 26, 2020 |
| Contact name |
Dawei Dai |
| E-mail(s) |
daweidai@ufl.edu
|
| Organization name |
University of Florida
|
| Department |
Horticultural Sciences
|
| Street address |
2550 Hull Rd
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32611 |
| Country |
USA |
| |
|
| Platform ID |
GPL25410 |
| Series (1) |
| GSE141324 |
Next generation sequencing facilitates quantitative analysis of maize 35 mitochondrial genes in dek53-ref and wild-type (WT) kernels |
|
| Relations |
| BioSample |
SAMN14930884 |
| SRA |
SRX8346538 |
