|
| Status |
Public on Sep 11, 2024 |
| Title |
Col-0_inflorescence_high RI_AGO1-RIP-TRM-sRNA-seq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
inflorescence
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: inflorescence
genotype: Col-0
ecotype: Col-0
library type: TRM-RIP-sRNA-seq
|
| Treatment protocol |
None
|
| Growth protocol |
The seeds were grown in soil. After cultivated in 4 ℃ for three days, the seeds were transferred to 16/8 h (light/dark) greenhouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from inflorescence tissues using TRIzol reagent (Invitrogen, USA) following standard protocols. For "conventional sRNA-seq" library, total RNA was separated in 16% denaturing PAGE gel to excise 18-30 nt, and gel purified RNA was treated by NaCl solution. For "NaIO4 treatment" library, total RNA was separated in 16% denaturing PAGE gel to excise 18-30 nt, and gel purified RNA was treated by NaIO4 solution. For "PBA-PAGE" library, total RNA was separated in 16% denaturing PAGE gel supplemented with 2% PBA to excise 18-30 nt, and gel purified RNA was treated by NaCl solution. For "TRM-sRNA-seq" library, total RNA was separated in 16% denaturing PAGE gel supplemented with 2% PBA to excise 18-30 nt, and gel purified RNA was treated by NaIO4 solution. For AGO1-RIP samples, protein was extracted from Col-0 inflorescence. After immunoprecipitation, AGO1-bound RNAs were isolated by phenol-chloroform extraction and ethanol precipitation.
All types of small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following manufacturer's instructions and purified using Monarch PCR & DNA kit (NEB, USA).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
AGO1 RIP high quality PBA+OX R1
immunoprecipitated RNA
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore (version 0.6.6).
Trimmed sequence reads were mapped to TAIR10 using ShortStack (version- 3.8.5 parameters- --align_only –nohp --mmap u --bowtie_m 1000 --ranmax 50 --mismatches 0).
Reads count extraction was performed using featureCounts (version- v2.0.1 parameters- -O --largestOverlap -fraction).
Reads count normalization was performed using DESeq2 and custom R scripts.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files include sequence counts for each Sample.
|
| |
|
| Submission date |
Sep 25, 2023 |
| Last update date |
Sep 11, 2024 |
| Contact name |
Susu Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Fudan university
|
| Street address |
2005 Songhu Rd. Yangpu District
|
| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE244009 |
An improved terminal ribose-modified small RNA sequencing (TRM-sRNA-seq) reveals novel features of miRNA modification and identifies HEN1-independent 2’-O-modified sRNAs derived from tRNAs |
|
| Relations |
| BioSample |
SAMN37537692 |
| SRA |
SRX21882982 |
