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Status |
Public on Jan 08, 2022 |
Title |
RNA-seq and sRNA-seq analysis of maize W22 lines containing B chromosomes |
Organism |
Zea mays |
Experiment type |
Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing
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Summary |
The maize B chromosome is a non-essential chromosome and is not detrimental to plant development at low copy numbers. Nondisjunction of the maize B chromosome occurs at the second pollen mitosis. Maize lines containing B chromosomes are widely used in a variety of studies, such as gene dosage effect, centromere function and engineering of artificial chromosomes etc. An understanding of how the B chromosome affect gene expression is required for utilizing the B chromosome as tools for genetic studies and engineering. Therefore, we performed RNA-seq and small-RNA seq experiments on maize lines containing one through seven copies of B chromosomes to examine how gene expression responds to change of B copy numbers.
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Overall design |
Maize lines W22 with B chromosomes were screened by Fluorescence in situ hybridization at their seedling stage for identification of B chromosomes. W22 lines with one through seven copies of B chromosomes were used as the experimental group whereas W22 lines without B chromosome were used as the control group for RNA-seq and small-RNA seq experiments. 2-4 biological replicates were used for each experimental or control conditions.
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Web link |
https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15665
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Contributor(s) |
Birchler JA, Shi X |
Citation(s) |
34997647 |
Submission date |
Feb 28, 2019 |
Last update date |
Jan 09, 2022 |
Contact name |
Xiaowen Shi |
Organization name |
Zhejiang University
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Department |
College of Agriculture and Biotechnology
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Lab |
Shi Lab
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Street address |
866 Yuhangtang Road NongshenghuanA443
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City |
Hangzhou |
State/province |
Zhejiang |
ZIP/Postal code |
310058 |
Country |
China |
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Platforms (1) |
GPL20156 |
Illumina NextSeq 500 (Zea mays) |
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Samples (56)
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Relations |
BioProject |
PRJNA524878 |
SRA |
SRP187091 |
Supplementary file |
Size |
Download |
File type/resource |
GSE127500_Counts_ERCC.txt.gz |
4.3 Kb |
(ftp)(http) |
TXT |
GSE127500_Counts_TE.txt.gz |
729.3 Kb |
(ftp)(http) |
TXT |
GSE127500_Counts_TE_RPKM.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
GSE127500_Counts_gene.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
GSE127500_Counts_miRNA.txt.gz |
9.0 Kb |
(ftp)(http) |
TXT |
GSE127500_Counts_miRNA_rpm.txt.gz |
17.4 Kb |
(ftp)(http) |
TXT |
GSE127500_DGE_analysis.txt.gz |
9.1 Mb |
(ftp)(http) |
TXT |
GSE127500_EdgeR_TE.txt.gz |
8.0 Mb |
(ftp)(http) |
TXT |
GSE127500_EdgeR_miRNA.txt.gz |
29.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |