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| Status |
Public on Jan 20, 2016 |
| Title |
rmr6-1 L D+S T0 R3 |
| Sample type |
SRA |
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| Source name |
youngest wrapped leaf
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| Organism |
Zea mays |
| Characteristics |
tissue: leaf
background strain: : B73
genotype: rmr6-1 mutant
treatment: drought plus salt
sampling time point: V5/V6 plants after 10 days of treatment
biological replicate: R3
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| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf and shoot apical meristematic area samples of four-five plants for each combination of genotype-treatment-sampling time point were pooled together, flash-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from frozen tissue using the Spectrum Plant Total RNA Kit (SIGMA), using "Protocol A" with 750µL of Binding Solution, to recover more of the small-sized RNA, and subjected to On-Column DNase Digestion (SIGMA).
The sRNA libraries were produced using the TruSeQ® small RNA Sample Preparation Kit (Illumina) and sequenced on an Illumina Hiseq2000 platform by the Istituto di Genomica Applicata (Udine, Italy).
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
3' and 5' adapters were removed with cutadapt ("-m 15 --discard-untrimmed" Martin, 2011).
Low complexity sequences, containing only two different nucleobases, were removed through a customized Perl script.
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to verify that in each library the Q score of the 90th percentile of reads was >= 28 across all bases.
The abundance of the unique sequences was obtained with a customized Perl script.
Genome_build: RefGen ZmB73 Assembly AGPv3
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: the first column is the sequence of the unique, non-redundant sRNA read, and the second column is its total raw abundance.
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| Submission date |
Jul 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael J Axtell |
| Organization name |
Penn State University
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| Department |
Department of Biology
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| Street address |
University Park
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| City |
State College |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platform ID |
GPL15463 |
| Series (1) |
| GSE70487 |
Genome-wide characterization of maize small RNA loci and their regulation in the required to maintain repression6-1 (rmr6-1) mutant and long-term abiotic stresses |
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| Relations |
| BioSample |
SAMN03838607 |
| SRA |
SRX1080241 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1782991_12-r3_rmr6_C4_T0_trim_filt.fastq_tag_count.txt.gz |
4.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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