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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 09, 2021 |
| Title |
ocl4 maize anthers, 0.4 to 0.7 mm, sterile phenotype (score = 0); sample ZOO 19 #23 (RNA-seq) |
| Sample type |
SRA |
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| Source name |
dissected maize whole anthers
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| Organism |
Zea mays |
| Characteristics |
genotype: ocl4 mutant
phenotype: sterile
tissue: anthers
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| Treatment protocol |
N/A
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| Growth protocol |
The maize plants 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). 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 and 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_AGPv4_genome
Supplementary_files_format_and_content: tag counts
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| Submission date |
May 12, 2020 |
| Last update date |
Sep 09, 2021 |
| 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 |
GPL15463 |
| Series (1) |
| GSE150446 |
HD-ZIP IV transcription factor OCL4 and 21-nt phasiRNAs are dispensable for male fertility in maize anthers |
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| Relations |
| BioSample |
SAMN14908244 |
| SRA |
SRX8334467 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4550678_ocl4_19_23_ms_S8_RC_chopped.txt.gz |
208.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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