|
| Status |
Public on Nov 27, 2013 |
| Title |
ra1_2mm_ear.1 |
| Sample type |
SRA |
| |
|
| Source name |
ear primordia
|
| Organism |
Zea mays |
| Characteristics |
tissue: pool of ra1 mutant ear primordia
Stage: 2mm
genotype: ra1/ra1 (in B73)
|
| Treatment protocol |
Ear and tassel tissues were dissected as described above in "overall design".
|
| Growth protocol |
For the wild-type ear and tassel developmental series, greenhouse-grown B73 inbred plants were used. For ramosa mutant series, segregating families (1:1) of ra1-R, ra2-R, and ra3-fea1 mutant alleles, all introgressed at least 6 times into the B73 inbred background, were grown at CSHL Uplands Farm. Field-grown plants were genotyped and collected 6-7 weeks after germination (V7-V8 stage).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNAeasy kit
RNA-seq libraries were constructed based on methods used in Li et al., Nature Genetics (2008)
RNA-seq libraries are paired end and are not strand-specific
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Libraries were quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip, and sequenced using the Illumina GAII platform at the CSHL Genome Center.
All image processing and base calling was done with the Illumina Real Time Analysis software on the HiSeq as the run progressed. Binary basecall files were then transferred to a shared Linux server for further processing and archival. The latest version of the Illumina processing software CASAVA was used to generate fastq files.
The Tuxedo suite (Trapnell et al. 2010) was used for mapping and analysis of RNA-seq data. Tophat (version 1.2.0) was used to align reads to the maize reference genome (AGPv2) based on an a priori set of 110,028 predicted maize gene models (Working Gene Set v5b.60; maizesequence.org). Cuffdiff (version 1.0.2) was used to analyze differential expression using a high-confidence subset of 39,656 maize gene models, the Filtered Gene Set (FGS v5b.60; maizeseqeunce.org). Gene-level expression values are represented by Fragments Per Kilobase exon per Million reads mapped (FPKM) and a consensus FPKM was determined for each gene based on its representation across biological replicates (Trapnell et al. 2010). Further details are provided in Supplemental Methods in associated Eveland et al. paper.
Genome_build: Zea mays refgen_agpv2
Supplementary_files_format_and_content: Processed data files from Cufflinks output can be found for each sample - FPKM values at both gene level and transcript isoform level are provided. Consolidated (combined) files from Cuffdiff output are also provided and give the FPKM values and 95% confidence intervals for expression of each gene across replicates and between developmental stages or genotypes. All are tab-delimited txt files.
|
| |
|
| Submission date |
Sep 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrea L Eveland |
| E-mail(s) |
aeveland@danforthcenter.org
|
| Organization name |
Donald Danforth Plant Science Center
|
| Street address |
975 N. Warson Road
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL9361 |
| Series (2) |
| GSE51047 |
Regulatory Modules Controlling Maize Inflorescence Architecture: mRNA-seq data |
| GSE51050 |
Regulatory Modules Controlling Maize Inflorescence Architecture |
|
| Relations |
| BioSample |
SAMN02360523 |
| SRA |
SRX357124 |
