|
| Status |
Public on Jul 06, 2020 |
| Title |
Col00Sh2 |
| Sample type |
SRA |
| |
|
| Source name |
Shoot
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: wild type
tissue: root
treatment: iron deficient
|
| Treatment protocol |
Grown for 3 days on iron sufficient (+Fe) or iron deficient (-Fe) media
|
| Growth protocol |
Germinated and grown for 12 days on B5, followed by 3 days on iron sufficient (+Fe) or iron deficient (-Fe) media; 16/8 light/dark cycle at 22°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fresh Arabidopsis root tissue using Plant RNA Isolation Kit (Agilent) per manufacturer's instructions.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Raw reads were filgered to remove reads containing adapters or reads of low quality, then mapped to Arabidopsis TAIR10 reference genome using TopHat2 (TMR>70%; MMR<10%)
RPKM (Reads Per Kilo bases per Million reads) method (Mortazavi et al 2008)
Genome_build: TAIR10
Supplementary_files_format_and_content: RPKM
|
| |
|
| Submission date |
May 04, 2020 |
| Last update date |
Jul 06, 2020 |
| Contact name |
Jeeyon Jeong |
| Organization name |
Amherst College
|
| Department |
Biology
|
| Lab |
Jeong
|
| Street address |
25 East Drive
|
| City |
Amherst |
| State/province |
MA |
| ZIP/Postal code |
01002 |
| Country |
USA |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE149816 |
PRC2-mediated H3K27me3 regulates iron homeostasis genes in the shoots of Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN14828731 |
| SRA |
SRX8245674 |
