|
| Status |
Public on May 16, 2014 |
| Title |
R118_RNASeq_Clark_defective |
| Sample type |
SRA |
| |
|
| Source name |
CD: 400-500mg seed weight stage
|
| Organism |
Glycine max |
| Characteristics |
cultivar: Clark
genotype/variation: Seed coat mutant
tissue: Seed coat (400-500mg seed weight stage)
|
| Treatment protocol |
optimal green house growth conditions
|
| Growth protocol |
Soybean plants (standard and defective seed coat isolines) were grown in the green house and the seeds were harvasted at different seed weight ranges. Seed coats from 50-100mg, 100-200mg and 400-500mg seed weight satges were dissected. All tissues were lyophillized and stored at -70C till further use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from Harosoy isolines was extracted using standard phenol-chloroform method with lithium chloride precipitation. Extraction of RNA from seed coats with dark pigmentation required the use of a modified extraction protocol which prevents procyanidins from binding the RNA based on the procedure from Wang et al. Plant Physiology, 1994.
Library construction and high-throughput sequencing was carried out using RNA-Seq technology with Illumina GAII and HiSeq2000 at the W. M. Keck Center for Comparative and Functional Genomics at the University of Illinois, Urbana-Champaign.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
R118_RNASeq_Clark_defective
|
| Data processing |
75 bp (from GAII) and 100bp (from HiSeq2000) reads were aligned to soybean reference genome cv. Williams 82 (phytozome v.4), using BOWTIE (Langmead et al., Genome Biology, 2009) with up to 3 mismatches and 25 alignments allowed.
RNA-Seq data was normalized in Reads per Kilobase of Gene Model Per Million Mapped Reads (RPKM) (Mortazavi et al., Nat Met 5:621-628, 2008).
Genome_build: Glycine max cv. Williams 82 (http://www.phytozome.net/soybean.php)
|
| |
|
| Submission date |
Feb 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lila O. Vodkin |
| E-mail(s) |
l-vodkin@illinois.edu
|
| Phone |
217-244-6147
|
| Organization name |
University of Illinois
|
| Department |
Crop Sciences
|
| Lab |
Lila Vodkin
|
| Street address |
1201 W. Gregory Dr.
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL15008 |
| Series (1) |
| GSE54903 |
RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts |
|
| Relations |
| BioSample |
SAMN02640338 |
| SRA |
SRX469883 |
