|
| Status |
Public on May 26, 2012 |
| Title |
Small RNAs from B73xMo17 shoot apex - 2007 expt |
| Sample type |
SRA |
| |
|
| Source name |
seedling shoot apex, B73xMo17
|
| Organism |
Zea mays |
| Characteristics |
genotype: B73xMo17
tissue: shoot apex
developmental stage: 11 days after sowing (3-4 leaf stage)
|
| Growth protocol |
Shoot apex samples were isolated from greenhouse-grown plants.
40 seeds were sown in a flat consisting of 1:1:1 soil, peat, perlite mix and grown in a greenhouse under 16 hours of light and 8 hours of dark during the fall of 2007.
Maize seedlings were cut at their root nodes. Coleoptiles and all tissue from fully emerged leaves were removed using a dissecting needle. Tissue enriched for leaf primordia and the shoot apex was isolated by cutting 1 cm above the base of the shoot.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol according to the maufacturer's protocols (Invitrogen). Quantification and quality checks of total RNA was performed by A260/A280 spectrophotometry using a Nanodrop ND-1000, gel electrophoresis, and total RNA Bioanalzyer chips (Agilent).
sRNA library construction was performed by the Michael Smith Genome Sciences Centre following the protocol of Lu et al. (2007) (PMID 17889797). sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced with Illumina SBS technology on an Illumina Genome Analyzer. Sequences with at least 5 reads were retained in the dataset.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
PERL scripts were designed or scripts from the FASTX toolkit (version 0.0.12) were used to sort multiplexed libraries according to their barcode, to remove the 3' adapter and its artifacts, to filter the 5' adapter, to collapse reads into distinct sequences and to calculate abundance.
sRNAs were aligned to B73 and Mo17 genomic sequences using Novoalign (V2.07.11).
The processed data file '2007_shoot_apex_abundance_file.txt' is available as a supplementary file from the Series record.
Genome builds: B73 genome, maizesequence.org release 4a.53 (October, 2009); Mo17 whole genome shotgun clones.
|
| |
|
| Submission date |
Apr 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wesley T Barber |
| E-mail(s) |
barber4@illinois.edu
|
| Organization name |
University of Illinois at Urbana-Champaign
|
| Department |
Department of Crop Sciences
|
| Lab |
Moose Maize Functional Genomics Lab
|
| Street address |
1201 W. Gregory Drive
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL9141 |
| Series (1) |
| GSE37411 |
Small RNA sequencing in maize hybrids and inbreds |
|
| Relations |
| SRA |
SRX143307 |
| BioSample |
SAMN00858172 |
