|
| Status |
Public on Jan 04, 2023 |
| Title |
Shoot_1%DMS_OsNRT2.3B |
| Sample type |
SRA |
| |
|
| Source name |
rice shoots
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: Shoot
age: Two-week-old
target: OsNRT2.3B
|
| Treatment protocol |
Two-week-old rice seedlings were collected and immersed in 20ml of 1X DMS reaction buffer (40mM HEPES pH7.5, 100mM KCl and 0.5mM MgCl2). 200µl of DMS was added to the reaction buffer to give a final concentration of 1%.The same volume of DEPC-treated water was added into the reaction buffer for the mock treatment. DMS treatment was performed for 15 min at 30°C with shaking at 250rpm.
|
| Growth protocol |
Two-week-old rice (Oryza sativa ssp.Nipponbare) seedlings grown in hydroponic nutrient solution
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DMS-treated or DMS-Untreated samples were pelleted and resuspended in 1 mL Trizol, RNA was extracted by phenol-chloroform extraction and isopropanol precipitation.
For target-specific DMS-MaPseq, 3 µg of DMS-treated sample was mixed with gene-specific RT primers. The reverse transcription was proceeded with TGIRT-III (Ingex). Then specific gene cDNA were amplified using KOD hot start DNA polymerase with gene-specific primers.The mixture was incubated under vacuum for 5 min at room temperature. The samples were then washed three times with 50 mL of DEPC-treated water each, frozen in liquid nitrogen, and ground to fine powder.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For filtering the raw fastq files, Trimmomatic was used to remove adapter sequences. A sliding window trimming approach was used to filter the reads with quality scores lower than 20. Next, 2 nt from the 5′ end of each read were trimmed, and the reads over 200 bp were kept for further analysis.
Reads were aligned to the reference sequence using TopHat with parameter setting: --library-type fr-unstranded --no-novel-juncs -N 25 --read-gap-length 7 --read-edit-dist 25 --max-insertion-length 5 --max-deletion-length 5 -g 3 --no-mixed.
Mismatch count and coverage in each nuclotide were called, and mismatches located within 3nt of an insertions or deletion were masked for future analysis.
Assembly: MSU Rice Genome Annotation Project Release 7
Supplementary files format and content: text files include mutation ratio in each nucleotide for each Sample.
|
| |
|
| Submission date |
Aug 02, 2022 |
| Last update date |
Jan 04, 2023 |
| Contact name |
Xiaorong Fan |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanjing Agricultural University
|
| Department |
1State Key Laboratory of Crop Genetics and Germplasm Enhancement
|
| Street address |
Nanjing city Wei Tong Road 6
|
| City |
Nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL27860 |
| Series (1) |
| GSE210296 |
High-temperature adaptation of an OsNRT2.3 allele is thermoregulated by small RNAs |
|
| Relations |
| BioSample |
SAMN30098132 |
| SRA |
SRX16768875 |
