|
| Status |
Public on Jan 28, 2015 |
| Title |
B73 starchy endopserm, biorep 2 (BS2) |
| Sample type |
SRA |
| |
|
| Source name |
endosperm
|
| Organism |
Zea mays |
| Characteristics |
cell type: Starchy endosperm
developmental stage: 15 DAP (days after pollination)
genotype: B73 (wild type)
|
| Treatment protocol |
Developing kernels were harvested at 15 DAP (days after pollination) fixed in Farmers fixative and embedded in paraffin. Endosperm cell types were isolated from sections using a Laser Capture Microdissection (LCM) microscope (PixCell II LCM System, Arcturus Engineering).
|
| Growth protocol |
Wild type (B73) and nkd mutant plants (fourth generation back cross to B73) were grown at the Iowa State University Curtiss research farm in the summer of 2012.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from captured cells using Arcturus Picopure RNA Isolation Kit (Life Technologies, Grand Island, NY, USA). The total RNA was subjected to a T7 RNA Polymerase based linear RNA amplification strategy, using TargetAmp™ 2-Round aRNA Amplification Kit 2.0 (Epicentre Biotechnologies, Madison, WI) to generate sufficient quantity of RNA as a template for RNA sequencing.
Transcript libraries were constructed using the TruSeq RNA sample preparation kit (Illumina).
The libraries were indexed (barcoded) using specific adapter sequences and were subjected to cluster analysis and 50 base pair paired end sequencing using an Illumina HiSeq2000 machine, by the Iowa State University DNA facility. 3 flow cells were used, each containing 1 biorep of the 4 tissue types (i.e. flow cell 1 contained BA1, NA1, BS1 and NS1).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The raw sequence data were first quality checked using the FastQC software
Reads were then aligned to the B73 reference maize genome assembly V2 using the Tophat short sequence aligner
Read counts were normalized based on library sizes and analyzed for differentially expressed genes using the DESeq software (Anders and Huber, 2010).
Genome_build: Maize AGPv2
Supplementary_files_format_and_content: The processed data is a microsoft excel file that contains normalised transcript read counts of wild type (B) and nkd (N) mutant aleurone (A) and starchy endosperm (S) samples.
|
| |
|
| Submission date |
Sep 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Philip W Becraft |
| Organization name |
Iowa State University
|
| Department |
Genetics, Development and Cell Biology
|
| Lab |
2188
|
| Street address |
Molecular Biology Building
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE61057 |
The naked endosperm genes encode duplicate ID domain transcription factors required for maize endosperm differentiation |
|
| Relations |
| BioSample |
SAMN03018464 |
| SRA |
SRX694825 |
