|
| Status |
Public on Jul 21, 2017 |
| Title |
407179T2CF Rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
leaf tissue, second trifoliate, sensitive, charcoal filtered
|
| Organism |
Glycine soja |
| Characteristics |
genotype: 407179
tissue: leaf
leaf position: Second trifoliate
treatment: Charcoal filtered
|
| Treatment protocol |
Plants were exposed to a 75 ppb ozone treatment for 7 hours alongside a charcoal-filtered control at < 10 ppb ozone.
|
| Growth protocol |
Plants were germinated in a charcoal-filtered greenhouse and moved to continuously stirred tank reactors (CSTRs) at 2 weeks in Raleigh, NC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Qiagen Plant RNeasy Mini Kit (Cat No./ID: 74904) with on-column DNase I digest.
Standard Illumina Protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Processed data file: gene_exp.diff
|
| Data processing |
Fast-X Toolkit was used to trim off adapters and remove low-quality reads (PHRED <= 33).
Aligned to soybean reference genome and supplied annotations Gmax_275_Wm82.a2.v1 using TopHat 2.0.13.
Transcript Assembly completed using Cufflinks 2.2.1.
Differential expression tested using cuffdiff 2.2.1 with parameters --max-bundle-frags 500000 -b -u
Genome_build: Gmax_275_Wm82.a2.v1
Supplementary_files_format_and_content: gene_exp.diff: Tab-delimited differential expression file using FPKM values.
|
| |
|
| Submission date |
Aug 03, 2016 |
| Last update date |
Jul 26, 2022 |
| Contact name |
Nathan Waldeck |
| E-mail(s) |
nathanwaldeck2022@u.northwestern.edu
|
| Organization name |
Northwestern University
|
| Street address |
303 E Superior St, Lurie 7-220
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL22279 |
| Series (1) |
| GSE85146 |
RNA-Seq Study Reveals Genetic Responses of Diverse Wild Soybean Accessions to Increased Ozone Levels |
|
| Relations |
| BioSample |
SAMN05509113 |
| SRA |
SRX1997414 |
