|
| Status |
Public on Mar 18, 2013 |
| Title |
R50_5-6mgCOT |
| Sample type |
SRA |
| |
|
| Source name |
cotyledon
|
| Organism |
Glycine max |
| Characteristics |
cultivar: Williams 43
Stage: 5-6mg fresh weight
preservation: fresh frozen
purification: none
|
| Growth protocol |
Plants were grown in optimal greenhouse conditions. Tissues were harvested at stated days after flowering or mg fresh weight. Whole seeds were divided by hand into cotyledons and seed coats for some samples.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tissues using phenol:chloroform and a lithium chloride precipitation (Gonzalez and Vodkin 2007). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina Genome Analyzer II or an Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Standard Illumina pipeline including CASSAVA
Sequenced reads were aligned to 78,773 Glyma1 cDNA soybean gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Genome_build: Glyma1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Dec 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Lila O. Vodkin |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE42871 |
Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity |
|
| Relations |
| Alternative to |
GSM3508915 |
| SRA |
SRX212258 |
| BioSample |
SAMN01832613 |
