|
| Status |
Public on Nov 06, 2024 |
| Title |
smRNA hda6ldl12 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 14 days seedling
ecotype: Col-0
tissue: seedling
genotype: hda6/ldl1/2
|
| Growth protocol |
Arabidopsis was grown in growth chambers under 12/12 h light/dark conditions at 22°C and harvested after 14 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For small RNA-seq, cells were lysed in Trizol and RNA extracted using standard methods.
Small RNA libraries were made using the Illumina TruSeq Small RNA Library kit according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
smRNA-seq reads were trimmed (removing sequencing adapter and low-quality reads) by using Cutadapt.
The clean reads were aligned to the Arabidopsis genome using Bowtie2, and sequences that did not perfectly align and those mapped to rRNAs, miRNAs, snRNAs, and tRNAs were discarded. The 24nt-siRNA sequences were extracted and normalized by calculating the 24nt-siRNA reads per million based on the total abundance of genome-matched 24nt-siRNA reads
Genome browser tracks were generated using deeptools (v 3.4.3) bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM)
Assembly: TAIR10
Supplementary files format and content: Processed data files are sequencing depth tracks (bigWig) obtained using bamCoverage (deepTools)
|
| |
|
| Submission date |
Oct 28, 2022 |
| Last update date |
Nov 06, 2024 |
| Contact name |
Pao-Yang Chen |
| Organization name |
Academia Sinica
|
| Department |
Institute of Plant and Microbial Biology
|
| Lab |
Pao-Yang Chen
|
| Street address |
128 Sec. 2, Academia Rd, Nankang,
|
| City |
Taipei |
| ZIP/Postal code |
115 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL21785 |
| Series (2) |
| GSE216788 |
Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [ncRNA-Seq] |
| GSE216789 |
Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 |
|
| Relations |
| BioSample |
SAMN31506911 |
| SRA |
SRX18061797 |
