|
| Status |
Public on Apr 11, 2019 |
| Title |
AC-3 |
| Sample type |
SRA |
| |
|
| Source name |
Mature Castor Seeds
|
| Organism |
Ricinus communis |
| Characteristics |
tissue: Seed
cultivar: Baker 296
Stage: Mature
tissue: Embryo
|
| Growth protocol |
Plants seeds were harvested from were grown at 22C in greenhouse conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a Hot Borate RNA extraction protocol
Library was prepared using the Illumina TrueSeq library preparation
Library insert size was ~300bp. Sequencing was 2X75 on a MidOutput Cassette for an Illumina NextSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Embryo3
ac3
|
| Data processing |
Data were cleaned using trimmomatic, removing adaptors, low quality bases with a sliding window of 4 and a Qscore<20, keeping reads > 25bp
Abundance measurements were done using Salmon, calling 100 bootsraps, validateMappings, and rangfactorizationbins (4)
Data were quantified using DESeq2
Genome_build: NCBI Ricinus communis Annotation Release 101
Supplementary_files_format_and_content: Salmon-coutsdata.txt, DESeq2-normalized_countstable.csv
|
| |
|
| Submission date |
Sep 07, 2018 |
| Last update date |
Apr 11, 2019 |
| Contact name |
Drew Sturtevant |
| E-mail(s) |
drewsturtevant@my.unt.edu
|
| Organization name |
University of North Texas
|
| Department |
BioDiscovery Institute
|
| Lab |
Kent Chapman Laboratory
|
| Street address |
155 Union Circle #305220
|
| City |
Denton |
| State/province |
TEXAS |
| ZIP/Postal code |
76203 |
| Country |
USA |
| |
|
| Platform ID |
GPL21641 |
| Series (1) |
| GSE119624 |
Tissue-Specific Differences in Metabolites and Transcripts Contribute to the Heterogeneity of Ricinoleic Acid Accumulation in Ricinus communis L. (castor) Seeds |
|
| Relations |
| BioSample |
SAMN09989026 |
| SRA |
SRX4653796 |
