|
| Status |
Public on Feb 13, 2014 |
| Title |
D99_25_50SC_BR1 |
| Sample type |
SRA |
| |
|
| Source name |
seed coat
|
| Organism |
Glycine max |
| Characteristics |
cultivar: Williams, PI548631
developmental stage: 25-50mg fresh weight
preservation: lyophilized
purification: none
tissue: seed coat
|
| 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.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tissues using phenol:chloroform and a ethanol precipitation. Sequencing was performed by the Keck Center (University of Illinois) using an Illumina Genome Analyzer II or an Illumina HiSeq 2000.
smRNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed by the Keck Center (University of Illinois) using Illumina Genome Analyzer II and Illumina HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
small RNA
|
| Data processing |
Adapter trimming was performed using Illumina’s Flicker pipeline which finds the presence of the adapter in each read by finding the best alignment of the adapter to the read, and removing it from the read.
After the seqeunces are trimmed, sequences are counted with excluding any sequences shorter than 16bp. Counting is the process of compressing a file of reads by listing reads uniquely together with a number representing how many times it occurred in the file.
Supplementary_files_format_and_content: Fasta files include counts of reads.
|
| |
|
| Submission date |
Jan 08, 2013 |
| 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) |
| GSE43348 |
The Transition from Primary siRNAs to Amplified Secondary siRNAs that Regulate Chalcone Synthase During Development of Glycine max Seed Coat |
|
| Relations |
| SRA |
SRX215533 |
| BioSample |
SAMN01883218 |
