|
| Status |
Public on Feb 28, 2023 |
| Title |
Pistil 2N, replicate 1, snRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
pistil
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
genotype: wild type
tissue: pistil
developmental stage: heading stage
|
| Growth protocol |
Rice (Oryza sativa ssp. Japonica cultivar Nipponbare) plants were grown in the potting soil mixed with sand in climate chambers with a relative humidity of 70%, under the following circadian rhythm: 10 h light at 30℃ and 14 h dark at 25℃.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Dissected pistils were frozen in liquid nitrogen and ground to powder. The powder was suspended by nucleus isolation buffer. Then, the crude nuclei were enriched from the slurry by applying 10 μm mini cell strainer, and were subsequently purified by PI-labeled FANS. The purified nuclei adjusted by the nucleus count were subjected to GEM partitioning
Library was performed according to the manufacter’s instructions. For 2N nuclei: Chromium Next GEM single cell 3’ v3.1 protocol, Rev_D, 10x Genomics. For 1N nuclei: Chromium Next GEM Single Cell 3' LT v3.1, protocol, 10x Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: IRGSP1.0
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Jul 18, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Hao Yu |
| Organization name |
National University of Singapore
|
| Street address |
16 Science Drive 4
|
| City |
Singapore |
| ZIP/Postal code |
117558 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL27860 |
| Series (2) |
| GSE208432 |
Single-nucleus sequencing deciphers lineage trajectories in rice pistils [snRNA-seq] |
| GSE208433 |
Single-nucleus sequencing deciphers developmental trajectories in rice pistils |
|
| Relations |
| BioSample |
SAMN29806140 |
| SRA |
SRX16335164 |
