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| Status |
Public on May 12, 2022 |
| Title |
3X_2C_3N4 |
| Sample type |
SRA |
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| Source name |
Leaf tissue
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| Organism |
Zea mays |
| Characteristics |
age: 45-day
diploid aneuploids, disomy, whole-ploidy, or b chromosome: whole-ploidy comparison(triploid)
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| Growth protocol |
45-day grown in the greenhouse
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extracted by mirVana™ miRNA Isolation Kit
sRNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
rpm_miRNA.txt
results_counts_miRNA.txt
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| Data processing |
1. the 3' end of the reads was trimmed for Illumina adapters, for ambiguous nucleotides (N's), and for artificial poly-G using cutadapt version 1.16.
2. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q33 -q20 -p80).
3. Reads mapped to known structural RNAs (rRNAs, tRNAs, sn-RNAs, and sno-RNAs) from Rfam 14.0 using bowtie 2 were removed.
4. Reads of 18-30 nt without poly(A) tails were aligned to the maize reference genome W22v2, the maize chloroplast, and mitochondrial genomes.
5. Read counts were normarlized with RPM and differential gene expression analysis were performed via edgeR.
Supplementary_files_format_and_content: Tab-delimited text files include raw count table of mapped miRNA generated by ShortStack and RPM normalized counts.
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| Submission date |
Nov 22, 2021 |
| Last update date |
May 12, 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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| Platform ID |
GPL20156 |
| Series (1) |
| GSE189317 |
Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize |
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| Relations |
| BioSample |
SAMN23408268 |
| SRA |
SRX13207614 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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