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| Status |
Public on Feb 11, 2015 |
| Title |
PARE library from Anther 1.0 and 1.5 mm |
| Sample type |
SRA |
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| Source name |
anther
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| Organism |
Zea mays subsp. mays |
| Characteristics |
genotype/variation: Wildtype (W23)
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| Growth protocol |
Fertile anthers of the W23 inbred line, mac1-Y211 and msca1 introgressed five times into W23, and ocl4 in the A188 inbred were grown in Stanford, CA under greenhouse conditions.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Tri reagent (Molecular Research Center, Cincinnati, OH) or Plant RNA Reagent (Invitrogen, Carlsbad, CA).
Small RNA and RNA-seq libraries were constructed using TruSeq™ Small RNA Sample Prep Kit and TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). PARE libraries were constructed as previously described. All libraries were sequenced on an Illumina Hi-Seq 2000 instrument at the Delaware Biotechnology Institute, Newark, DE.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
All reads from small RNA, PARE or RNA-seq libraries were trimmed to remove adapter sequences using a Perl script. After trimming off adapters, small RNA reads with the length between 18 and 34 were kept; PARE reads that are longer than 21-nt are discarded, and 21-nt PARE reads are chopped to 20-nt by removing the last nucleotide. Small RNA and PARE reads were mapped to the reference genome using bowtie, and RNA-seq reads were mapped using Tophat. We developed three websites and databases (for sRNA, PARE and RNA-seq, respectively) using the Maize AGPv2 genome, to store and analyze all libraries; we used these visualization tools extensively for this analysis. These Web sites are available at http://mpss.udel.edu/maize_sRNA2/ , http://mpss.udel.edu/maize_RNAseq2/ and http://mpss.udel.edu/maize_pare/
Genome_build: MAIZE_AGPv2_genome
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| Submission date |
Nov 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Blake C. Meyers |
| E-mail(s) |
bmeyers@danforthcenter.org
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| Phone |
314-587-1422
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| Organization name |
Donald Danforth Plant Science Center
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| Lab |
Meyers lab
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| Street address |
975 N Warson Road
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
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| Platform ID |
GPL17914 |
| Series (2) |
| GSE52297 |
Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (PARE) |
| GSE52318 |
Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction |
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| Relations |
| BioSample |
SAMN02401803 |
| SRA |
SRX376787 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1262610_1_0w1_5.txt.gz |
60.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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