|
| Status |
Public on Jun 17, 2014 |
| Title |
B73 CSE 6DAP rep2 |
| Sample type |
SRA |
| |
|
| Source name |
endosperm
|
| Organism |
Zea mays |
| Characteristics |
strain: B73
tissue: central starchy endosperm
age: 6 DAP
|
| Growth protocol |
Plants of the reference maize genotype, B73, were grown under greenhouse conditions (16-h day) at the University of Arizona during January-June 2011, and self-pollinated to obtain 6-DAP kernels for laser-capture microdissection of the RNA.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from laser-capture microdissected sections using an ARCTURUS PicoPure RNA Isolation Kit (Applied Biosystems), and treated with DNase (TURBO DNase, Ambion) before amplification.
Standard barcoded RNA-seq libraries were generated to facilitate sequencing of four samples using a single Illumina flowcell lane. Libraries were generated using protocols adapted from Illumina mRNA sample preparation protocol (cat. no 1004894 Rev.A).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
amplified poly-A RNA
|
| Data processing |
Illumina Genome Analyzer IIx System
Sequenced reads were mapped to maize reference genome using Tophat1 with default parameters
Number of reads mapped to each gene were quantified by the intersectBed function implemented in the BEDTools package, and normalized by total count normalization method.
Genome_build: ZmB73_RefGen_v2.tar.gz
Supplementary_files_format_and_content: tab-delimited text files include count-based values for each gene
|
| |
|
| Submission date |
Jun 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ramin Yadegari |
| E-mail(s) |
[email protected]
|
| Phone |
520-621-1616
|
| Organization name |
University of Arizona
|
| Department |
Plant Sciences
|
| Lab |
Yadegari
|
| Street address |
1140 E. South Campus Dr.
|
| City |
Tucson |
| State/province |
Arizona |
| ZIP/Postal code |
85721 |
| Country |
USA |
| |
|
| Platform ID |
GPL13977 |
| Series (1) |
| GSE58504 |
RNA-Seq Analysis of Laser-Capture Microdissected Cells of the Developing Central Starchy Endosperm of Maize |
|
| Relations |
| BioSample |
SAMN02862034 |
| SRA |
SRX599933 |
