|
| Status |
Public on Aug 08, 2023 |
| Title |
arabidopsis_1d_wl_a |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root
ecotype/cultivar: Col-0
treatment: unshaded root 1d
|
| Growth protocol |
Arabidopsis seedlings were grown in half-strength MS agar plates under constant white light for 5 days and subsequently kept in unshaded conditions or transfered to shade for the indicated time. Roots were harvested and immediately frozen in liquid nitrogen for RNA extraction. Tomato seedlings were grown in white light for 7 days under the same conditions and treatments described for Arabidopsis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Arabidopsis total RNA was extracted with trizol-chloroform protocol. Tomato total RNA was extracted with a Promega ReliaPrep RNA miniprep System following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
arabidopsis_FPKM.csv
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, then mapped to either TAIR10 or ITAG4.1 whole genome using star v2.7.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated with cufflinks v2.1.1.
|
| |
|
| Submission date |
Jun 10, 2021 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Ullas V. Pedmale |
| E-mail(s) |
pedmale@cshl.edu
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Department |
Pedmale
|
| Lab |
Pedmale Lab
|
| Street address |
1 Bungtown RD
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE175963 |
Whole-genome transcriptome analysis of tomato and Arabidopsis roots in the shade |
|
| Relations |
| BioSample |
SAMN19659179 |
| SRA |
SRX11116525 |
