|
| Status |
Public on Feb 02, 2021 |
| Title |
Dp4_4D_rep3[RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Leaf tissue
|
| Organism |
Zea mays |
| Characteristics |
age: 45-day
group (aneuploidy vs. whole-ploidy): aneuploidy comparison (Dp4)
|
| Growth protocol |
45-day grown in the greenhouse
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted by mirVana™ miRNA Isolation Kit; DNA extracted by DNeasy Plant Mini Kit (QIAGEN)
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Dp4_22C_5
diff_Dp4.txt
|
| Data processing |
mRNA-seq: Adaptors at the 3' end of the reads were trimmed using cutadapt version 1.16. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q 33 -q 20 -p 80). mRNA reads were aligned to ERCC sequences using Bowtie 2 with default parameters. The remaining non-ERCC reads were aligned to maize chloroplast and mitochondrial genome using TopHat2 with default parameters so that the organellar transcripts are excluded for further study. The remaining reads were then mapped to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using TopHat2 with default parameters. Normalized read counts were generated by Cuffdiff (--raw-mapped-norm) for each comparison.
DNA-seq: Adaptor trimming and low-quality read removal were performed the same as in mRNA-seq data process. Then the remaining DNA reads were aligned to the maize reference genome W22v2 along with the maize chloroplast and mitochondrial genome using Bowtie 2 with default parameters. A custom perl script was used for extraction of uniquely mapped read counts, which were then subjected to RPKM normalization.
Genome_build: W22v2 along with the maize chloroplast and mitochondrial genome (Springer et al., 2018; Bosacchi et al., 2015; Clifton et al., 2004).
Supplementary_files_format_and_content: Tab-delimited text files including tables showing cuffdiff normalized counts and differential gene expression analyses (mRNA-seq) and tables reporting RPKM normalized counts in DNA-seq.
|
| |
|
| Submission date |
Apr 23, 2020 |
| Last update date |
Feb 02, 2021 |
| Contact name |
Xiaowen Shi |
| Organization name |
Zhejiang University
|
| Department |
College of Agriculture and Biotechnology
|
| Lab |
Shi Lab
|
| Street address |
866 Yuhangtang Road NongshenghuanA443
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL25410 |
| Series (1) |
| GSE149186 |
Genomic imbalance determines positive and negative modulation of gene expression in diploid maize |
|
| Relations |
| BioSample |
SAMN14677565 |
| SRA |
SRX8162608 |
