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| Status |
Public on Dec 05, 2016 |
| Title |
RNAseq ms23 maize anthers, line 610_16 (sterile), 1.0 mm |
| Sample type |
SRA |
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| Source name |
RNAseq ms23 maize anthers, line 610_16
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| Organism |
Zea mays |
| Characteristics |
line: line 610_16 (sterile)
genotype/variation: ms23 mutant
tissue: anther
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| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA libraries and RNA-seq libraries were constructed from total RNA isolated from anthers of Zea mays using Plant RNA Reagent (Invitrogen, Life Technologies, USA). The sRNA library preparation protocol is based on Illumina’s sRNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA). And the RNA-seq library preparation protocol is based on Illumina’s TruSeq RNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA) The libraries were sequenced on an Illumina HiSeq 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 2500 |
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| Description |
1_0ms23_r2_RNAseq
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| Data processing |
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the maize genome (Maize Genome Database).
RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 50 nucleotides. RNA-seq reads were mapped to the maize genome (Maize Genome Database).
Genome_build: ZmaysB73_wgs_1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000275765.1)
Supplementary_files_format_and_content: Text containing distinct smallRNA's and RNA-seq reads with their raw abundance after removing the adapter sequences
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| Submission date |
Dec 04, 2016 |
| 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 |
GPL17628 |
| Series (1) |
| GSE90849 |
Characterization of small RNAs and genes in maize anthers (ms23 sterile) |
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| Relations |
| BioSample |
SAMN06108409 |
| SRA |
SRX2394518 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2415856_1_0ms23_r2_RNAseq_chopped.txt.gz |
218.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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