|
| Status |
Public on Nov 20, 2009 |
| Title |
mop1/mop1-SAM |
| Sample type |
SRA |
| |
|
| Source name |
Shoot apical meristem
|
| Organism |
Zea mays |
| Characteristics |
genotype: mop1/mop1 (mutant)
age: 14 days after planting
stage: 14-day after planting
|
| Treatment protocol |
Two genotypes compared without treatment
|
| Growth protocol |
kernels planted in growth chambers (PGW-40, Percival Scientific, http://www.percival-scientific.com). Temperature and light cycle were set as 25 degrees for 15 hours of light and 20 degrees for 9 hours of dark. During the light period the light intensity at the surface of the growth medium was maintained between 650 and 800 umol m-2 sec -1.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
At 14-days after planting SAMs were collected using the PALM MicroBeam System (115V Z, P.A.L.M. Microlaser Technologies, http://www.palm-microlaser.com.). Plants homozygous and heterozygous for the mop1-1 mutant allele were distinguished using two pairs of primers: a pair of mop1-specific primers consisting of RDRF3 (sequence: 5’-TCTCCACCGCCCACTTGAT-3’) and RDRR2 (sequence: 5’-ATGGCCAGCAGGGTGTCGCAGAT-3’) and a primer pair consisting of the Mutator TIR primer Mu-TIR (5’-AGA GAA GCC AAC GCC AWC GCC TCY ATT TCG TC-3’) and the mop1-specific primer RDRF3. Twelve mop1-1/mop1-1 and ten Mop1/mop1-1 SAMs were used to form mop1 and non-mutant pools. Collected SAM tissues were used for RNA extraction, RNA amplification and synthesis of double stranded cDNAs according to our previous published procedures (Ohstu, et al., 2007). These procedures preferentially target polyadenylated transcripts.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
SAM gene expression in mop1 mutants
mRNA was amplified from SAM tissue
|
| Data processing |
The Illumina reads were aligned to maize gene models (Release 4a.53, http://www.maizesequence.org) with short read aligner NOVOALIGN (http://www.novocraft.com). Two mismatches across 35 bp were allowed and only the reads that uniquely mapped to gene models were considered for further analysis.
There are two samples in the experiment: mop1-mutant vs. mop1-non-mutant.
Each sample has two techincal Solexa runs. The processed data for each sample is the merged data for final analysis across the technical reps for each sample.
|
| |
|
| Submission date |
Jun 23, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick S. Schnable |
| E-mail(s) |
schnable@iastate.edu
|
| Phone |
515-294-0975
|
| Organization name |
Iowa State University
|
| Street address |
2035B Roy J Carver Co-Lab
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL9141 |
| Series (1) |
| GSE16789 |
Expression of genes and transposons in mop1 mutants and non-mutants |
|
| Relations |
| SRA |
SRX014790 |
| BioSample |
SAMN00006971 |
