PRJNA1193632: Bulk RNA sequencing data of rice roots protoplasted for 2.5 hours and 3 hours, as well as rice roots grown in gel, non-compacted soil and compacted soil conditions
概要: We report raw bulk RNA sequencing data rice roots (X.kitaake) protoplasted for 2.5 hours and 3 hours to eliminate the effects of protoplasting duration on our scRNA-seq analysis, as well as rice roots grown in gel, non-compacted soil and compacted soil conditions to verify our findsing with scRNA-seq studies
项目整体设计: Bulk RNA-seq of 4 wild type (X.kitaake) grown in gel conditions, 3 wilde type grown in non-compacted soil conditions and 3 wild type grown in compacted soil conditions, 2 wild type with 2.5 hours protoplasting and 3 wild type with 3 hours protoplasting.
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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. |
| 处理方案: |
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| 提取方案: |
For RNA isolation, root tips were ground to a fine powder in liquid nitrogen using a mortar and pestle, followed by the addition of 1 ml of RLT buffer to the powdered tissue. RNA was then isolated and purified using the RNeasy Mini Kit (QiagenTM) according to the manufacturer’s protocol. |
| 建库方案: |
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification, with Novogene NGS RNA Library Prep Set. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. |
| 分子类型: |
Poly(A)+ RNA |
| 库的片段类型: |
PAIRED |
| 库的链类型: |
- |
| 测序平台: |
ILLUMINA |
| 测序仪型号: |
Illumina NovaSeq 6046; Illumina NovaSeq 6047; Illumina NovaSeq 6048; Illumina NovaSeq 6049; Illumina NovaSeq 6050; Illumina NovaSeq 6051; Illumina NovaSeq 6052; Illumina NovaSeq 6053; Illumina NovaSeq 6054; Illumina NovaSeq 6055; Illumina NovaSeq 6056; Illumina NovaSeq 6057; Illumina NovaSeq 6058; Illumina NovaSeq 6059; Illumina NovaSeq 6060 |
| 链特异性: |
Unspecific |
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