|
| Status |
Public on Mar 03, 2024 |
| Title |
Rice root cells - bulk-Meristem-5 |
| Sample type |
SRA |
| |
|
| Source name |
Root
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: Root
cell type: All cell types of root
genotype: WT
developmental stage: Meristem
|
| Growth protocol |
X.kitaake was used as wild type. Rice seeds were dehulled, sterilized with 50% bleach for 10 min, and rinsed four to five times with sterile water. All plant growth was in Yoshida’s nutrient solution solidified with gellan gum (Gelzan, Caisson Inc).Growth boxes were kept at 4°C in the dark for 2-3 days until the seeds germinate, then transferred to a percival growth chamber set to 28°C, and consistant light. Rice seedlings were grown in the percival for 1-3 days before harvesting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sections (root tip to end of lateral root cap: Meristem; end of lateral root cap to the start of root hair elongation: Elongation; 1mm each beyond the start of root hair elongation: Maturation1 and Maturation2) were harvested into 10 μL RNA-later (Ambion) in the lid of a 1.5 ml tube. Samples were frozen in liquid nitrogen and stored at −80.and then processed by grinding with a blue homogenization pestle. RNA was isolated using the Zymo MagBead RNA Isolation kit according to the manufacturer’s protocol (Zymo).
RNA was used as input into the Lexogen QuantSeq 3′ FWD RNA-Seq library preparation procedure according to the manufacturer’s protocol, using the Unique Molecular Identifier (UMI) PCR add-on kit. Libraries were indexed and pooled on an Illumina NextSeq.
Lexogen QuantSeq 3′ FWD RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Lexogen QuantSeq 3′ FWD RNA-Seq
|
| Data processing |
Reads were aligned to Michigan State University Rice genome v7 with the STAR aligner, deduplicated using UMI-Tools, and counted with HTSeq-Count.
The BAM_COUNTS file were then merged. Reads were normalized, averaged and converted to Log(CPM) with EdgeR
Assembly: MSU 7.0
Supplementary files format and content: BAM_COUNTS file: HTSeq-Count processed file for each sample
Supplementary files format and content: xlsx file: Integrated and normalized averaged-reads for each gene caculated separately in different root sections
|
| |
|
| Submission date |
Mar 01, 2024 |
| Last update date |
Mar 03, 2024 |
| Contact name |
Philip Benfey |
| E-mail(s) |
[email protected]
|
| Organization name |
Duke University
|
| Street address |
124 Science Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL21087 |
| Series (1) |
| GSE260671 |
Bulk RNA sequencing data of rice root sections for Single-cell RNA-seq developmental stage annotation |
|
| Relations |
| BioSample |
SAMN40215596 |
| SRA |
SRX23809338 |
