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| Status |
Public on Jan 17, 2014 |
| Title |
B73 2DAP |
| Sample type |
SRA |
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| Source name |
kernel
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| Organism |
Zea mays |
| Characteristics |
cultivar: B73
age: 2 DAP
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| Growth protocol |
Plants of the reference maize genotype, B73, were grown under greenhouse conditions (16-hour day) at the University of Arizona during August-September 2009. All kernel and endosperm samples were collected from self-pollinated ovules. Self-pollinations were performed essentially as described by Poehlman (1977). The 0-, 2-, 3-, 4-, and 6-DAP kernels were collected by pushing down the glumes and pinching off the kernel at its base using a pair of forceps. The 8-, 10-, and 12-DAP endosperm samples were harvested by removing all tissues of the kernel from the pedicel up to the hilar region and cutting open the pericarp along the edge of the hilar region to expose and extract the endosperm free of the embryo and the pericarp using a surgical blade. In all cases, the staged kernels and endosperm samples were frozen immediately in liquid nitrogen and stored at -70°C before RNA extractions were carried out. Of the three individual biological replicates of each developmental stage collected for this work, one (bio-rep 1, except for 0 DAP where two technical replicates were sequenced) was used for RNA-Seq and all three were used for qRT-PCR analyses.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a SDS-Phenol method (Shirzadegan et al., 1991) except that 50-ml Phase-Lock-Gel Light Tubes (5Prime, Inc., Gaithersburg, MD, USA) were used to facilitate the phenol/chloroform extractions. Genomic DNA was removed using TURBO DNase I (Ambion) and RNA was further purified using RNeasy columns (Qiagen). For RNA-Seq analysis, two rounds of PolyA+ mRNA selection was carried out on 500 μg of total RNA using the Poly(A)PuristTM MAG kit (Ambion). RNA was quantified using a Nanodrop 1000 Spectrophotometer (Thermo Scientific, Inc., Wilmington, DE, USA), and RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA) found to be 9.3 to 10 in RNA integrity number (RIN).
RNA libraries were prepared for sequencing using standard protocols for SOLiD™ 4 System (Applied Biosystems)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
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| Data processing |
SOLiD™ System
Sequenced reads were mapped to maize reference genome using tophat1 with default parameters
Gene expression level was estimated as the sum of all reads mapped to the whole gene region using the intersectBed command implemented in the BEDTools package.
Genome_build: ZmB73_RefGen_v2.tar.gz; http://ftp.maizesequence.org/current/assembly/
Supplementary_files_format_and_content: tab-delimited text files include count-based values for each gene
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| Submission date |
Jan 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ramin Yadegari |
| E-mail(s) |
yadegari@email.arizona.edu
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| Phone |
520-621-1616
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| Organization name |
University of Arizona
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| Department |
Plant Sciences
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| Lab |
Yadegari
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| Street address |
1140 E. South Campus Dr.
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| City |
Tucson |
| State/province |
Arizona |
| ZIP/Postal code |
85721 |
| Country |
USA |
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| Platform ID |
GPL18179 |
| Series (1) |
| GSE54131 |
Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing |
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| Relations |
| BioSample |
SAMN02585256 |
| SRA |
SRX434342 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1308529_DAP2.txt.gz |
527.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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