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| Status |
Public on Feb 09, 2016 |
| Title |
pollen R1 |
| Sample type |
SRA |
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| Source name |
mature pollen
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| Organism |
Zea mays |
| Characteristics |
genotype: B73
treatment: control, greenhouse conditions
sampling time point: mature pollen, collected before 9AM
biological replicate: R1
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| Extracted molecule |
total RNA |
| Extraction protocol |
For each tissue, samples from three-four plants were pooled together, flash-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from frozen tissue with Trizol and small RNA extracted with PAGE gel.
The sRNA libraries were produced using the TruSeQ® small RNA Sample Preparation Kit (Illumina) and sequenced on an Illumina HiSeq 2500 platform
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
cutadapt was used to remove the 3' adapter (--discard-untrimmed -m 15) and to discard reads containing the 5' adapter
Low quality reads were removed with FASTX-Toolkit (-q 20 -p 85 -Q 33 -v)
Reads were aligned to the maize genome with ShortStack 3.3
Genome_build: (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, the second column is its total raw abundance
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| Submission date |
Feb 08, 2016 |
| 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 |
GPL17628 |
| Series (1) |
| GSE77657 |
Reference annotation for small RNA-producing genes in maize |
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| Relations |
| BioSample |
SAMN04479320 |
| SRA |
SRX1564782 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2055769_Pollen_R1_tag_count.txt.gz |
11.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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