|
| Status |
Public on May 26, 2012 |
| Title |
Small RNAs from B73 developing ear - low N |
| Sample type |
SRA |
| |
|
| Source name |
female inflorescence, B73
|
| Organism |
Zea mays |
| Characteristics |
genotype: B73
tissue: developing ear
developmental stage: V12 growth stage
|
| Growth protocol |
Developing ear samples were isolated from field-grown plants.
Tissue was collected from field-grown plots that were part of a larger yield-trial experiment where inbreds and hybrids were grown in separate blocks that were split by nitrogen fertilizer treatment (Summer, 2009, Urbana, IL). 40 seeds were sown per 3.6 m row, and rows were spaced 76 cm apart. 4 rows were sown per genotype. Plot was not supplemented with nitrogen.
The top developing ear was excised.
|
| 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 according to the instructions of the Illumina Small RNA kit version 1.5. sRNA was size selected in the 10- to 40-nt range. The sRNA library was sequenced as part of a multiplex of libraries (barcode=TGAC) on an Illumina Genome Analyzer. Sequences with an abundance of at least 1 read per million 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 'low_N_developing_ear_abundance_file.txt' file 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 |
SRX143314 |
| BioSample |
SAMN00858179 |
