|
| Status |
Public on Mar 01, 2023 |
| Title |
Well-watered 48 h cotton primary root tip replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Cotton Primary Root Tip
|
| Organism |
Gossypium hirsutum |
| Characteristics |
tissue: Root
genotype: AU90810
|
| Treatment protocol |
The media were set at water potentials of -0.02 MPa (well-watered treatments, WW), -1.0 MPa (water-stressed treatments, WS), which were obtained by mixing with certain amounts of 1 mM CaSO4. No further water supplies were added after the transplanting.
|
| Growth protocol |
Cotton (cv. AU90810) seedlings were cultivated in a vermiculite culture system at well-watered (WW) and water-stressed (WS) treatments. Seedlings were grown at 29 oC and near-saturation humidity in a dark growth chamber until harvest. The root tips of cotton were harvested at 24 h and 48 h after transplanting to well-watered or water-stressed media. Transplanting and harvesting were performed using a green ‘safe’ light. Root tips containing the whole elongation zones of cotton (12 mm for WW; 6 mm for WS) primary roots were collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cotton root tip samples (12 mm for WW; 6 mm for WS) were collected from seedlings and immediately frozen in liquid nitrogen and pooled to generate 50-100 mg FW per sample. Total RNA was isolated using Qigen Plant RNeasy mini kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing were performed by MU Genomics Technology Core
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Gossypium hirsutum NAU-NBT v1.1 whole genome using Hisat2 (v1.0).
Read counts were calculated using Htseq-count (v0.6.1), counting how many aligned reads overlap the exon of each gene (Anders et al., 2015).
Assembly: Gossypium hirsutum NAU-NBT v1.1
Supplementary files format and content: Matrix tables for raw counts for all samples
|
| |
|
| Submission date |
Dec 19, 2022 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Sidharth Sen |
| E-mail(s) |
ssz74@mail.missouri.edu
|
| Organization name |
University of Missouri
|
| Department |
The Division of Plant Sciences and Technology
|
| Lab |
Sharp Lab
|
| Street address |
Agriculture Bldg, University of Missouri
|
| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65201 |
| Country |
USA |
| |
|
| Platform ID |
GPL27127 |
| Series (2) |
| GSE221295 |
Differential regulation of primary root growth during water-deficit stress in cotton |
| GSE221296 |
Differential regulation of primary root growth during water-deficit stress |
|
| Relations |
| BioSample |
SAMN32308776 |
| SRA |
SRX18769802 |
