 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 26, 2013 |
| Title |
MXB 7DAP |
| Sample type |
SRA |
| |
|
| Source name |
maize
|
| Organism |
Zea mays |
| Characteristics |
tissue: endosperm
age: 7DAP
genotype/variation: Mo17XB73
|
| Growth protocol |
Maize B73 and Mo17 inbred lines were grown under greenhouse conditions. Reciprocal crosses and self-pollination were performed as follows: the ears were bagged before silking; when the silks grew to approximately 2 to 3 cm long, the ears were cut at 2cm from the top and the tassels were bagged. Pollination was conducted on the next day using the corresponding pollen. The un-pollinated kernels (0-DAP) and the kernels from the reciprocal crosses of B73 and Mo17 at 3, 5, 7, 10, and 15-DAP were harvested. Endosperm tissues from the 7, 10, and 15-DAP kernels were manually isolated. The endosperm and kernel were harvested from three different ears as three biological replicates and were immediately frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated from the 36 (12 samples × 3 replicates) groups of plant material using the Trizol method according to the manufacturer’s instructions.
18-30 nts RNAs were gel-purified from total RNA sample, Illumina 5’ and 3’ RNA adapter were sequentially ligated to the RNA fragments and the ligated products were size-selected on denaturing polyacrylamide gels. The adapter-linked RNA was reverse transcribed with small RNA RT primers and amplified with 15 cycles of PCR using small RNA PCR primer 1 and 2 (Illumina). The libraries were sequenced with the Illumina Genome Analyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Illumina RTA software used for basecalling.
Raw sequence reads were processed into clean full-length reads using the BGI small RNA pipeline. First, all low-quality reads were removed from the raw sequence, and the 3' adapter reads, 5' adapter contaminants, sequences containing the polyA tail and those smaller than 18 nt were also discarded. The remaining high-quality sequences were counted, and the unique sequences with their associated read counts were mapped to the maize genome to infer siRNA loci.
Genome_build: ZmB73_RefGen_v2.tar.gz
Supplementary_files_format_and_content: Compressed tab-delimited text files include counts and length for each sequence
|
| |
|
| Submission date |
Nov 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiangfeng Wang |
| Organization name |
University of Arizona
|
| Department |
School of Plant Sciences
|
| Street address |
1140 E. South Campus Drive, Marley Building 541C
|
| City |
Tucson |
| ZIP/Postal code |
85721 |
| Country |
USA |
| |
|
| Platform ID |
GPL9141 |
| Series (1) |
| GSE52726 |
Dynamic and Parent-of-Origin Expression of Small RNAs in the Developing Maize Endosperm |
|
| Relations |
| BioSample |
SAMN02420432 |
| SRA |
SRX383831 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1274881_M7.txt.gz |
86.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
