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Series GSE127500 Query DataSets for GSE127500
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
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.
 
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.
Web link https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15665
 
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
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
 
Platforms (1)
GPL20156 Illumina NextSeq 500 (Zea mays)
Samples (56)
GSM3635544 Control rep1 [RNA-Seq]
GSM3635545 Control rep2 [RNA-Seq]
GSM3635546 Control rep3 [RNA-Seq]
Relations
BioProject PRJNA524878
SRA SRP187091

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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Raw data are available in SRA
Processed data are available on Series record

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