|
Status |
Public on May 16, 2014 |
Title |
R115_RNASeq_Harosoy_standard |
Sample type |
SRA |
|
|
Source name |
HS: 50-100mg seed weight stage
|
Organism |
Glycine max |
Characteristics |
cultivar: Harosoy genotype/variation: Seed coat wild-type tissue: Seed coat (50-100mg 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 |
R115_RNASeq_Harosoy_standard
|
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 |
SAMN02640344 |
SRA |
SRX469884 |