|
| Status |
Public on Oct 16, 2020 |
| Title |
SC Clark 63 (UC7_PI548532) 50-100 mg rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Extended hilum region of seed coats (50-100 mg seed weight stage)
|
| Organism |
Glycine max |
| Characteristics |
plant introduction number: PI548532
repeat number: Repeat 1
|
| Treatment protocol |
optimal green house growth conditions
|
| Growth protocol |
Soybean plants (standard (UC7) and minute-hilum (mi) isoline (UC413) lines) were grown in the green house. Seeds of different weight ranges (10-25, 25-50 and 50-75 mg) were collected and hilum-containing seed coat regions were dissected. All tissues were lyophillized and stored at -70C till further use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from standard UC7 and mutant UC413 lines was extracted using standard phenol-chloroform method with lithium chloride precipitation (McCarty 1986).
Library construction with TruSeq RNA Sample Kit or Stranded TruSeq RNA Sample Kit and high-throughput sequencing was carried out using RNA-Seq technology with a Illumina 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 |
R131_UC7EH50
|
| Data processing |
Standard Illumina pipeline including CASSAVA
Sequenced reads were aligned to 88,647 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: Glycine max cv. Williams 82 (http://www.phytozome.net/soybean.php)
Supplementary_files_format_and_content: a tab-delimited text file includes RPKM values for each of the 20 samples and also annotations of the Glyma models from Phytozome
|
| |
|
| Submission date |
Mar 03, 2020 |
| Last update date |
Oct 16, 2020 |
| 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) |
| GSE146287 |
Overexpression of an ethylene-forming ACC Oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max |
|
| Relations |
| BioSample |
SAMN14277278 |
| SRA |
SRX7831744 |
