|
| Status |
Public on Aug 08, 2021 |
| Title |
35S.EVD.Col-0 sRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
inflorescence
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: inflorescence
overexpression: EVD
rna isolation: TRIzol
library preparation: Lexogen small RNA kit
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the standard TRIzol method or with the TRaPR isolation method.
Libraries were prepared with TRIzol or TRaPR isolated RNA with the TRUseq or Lexogen sRNA library preparation kits or with a custom library preparation protocol.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
sRNA
normalized_counts_sRNA.csv
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Trimming of reads with bbduk v. 37.66.
Mapping to the Arabidopsis thaliana genome (TAIR10) with STAR v. 020201.
Read counting with Rsubread 1.26.1.
Read normalization with DEseq2.
P-site occupancies estimation of RIBO-seq data using RiboProfiling.
Genome_build: TAIR10
Supplementary_files_format_and_content: normalized_counts_sRNA.csv: Comma-separated text file of log2 normalized read counts.
Supplementary_files_format_and_content: RiboSeq_transcript_counts.csv: Comma-separated text file of P-site counts per codon position along all coding sequences.
|
| |
|
| Submission date |
Feb 24, 2021 |
| Last update date |
Aug 08, 2021 |
| Contact name |
Stefan Oberlin |
| E-mail(s) |
stefan.oberlin@ucsf.edu
|
| Organization name |
ETH Zürich
|
| Department |
Department of Biology
|
| Street address |
Universitätstrasse 2
|
| City |
Zürich |
| ZIP/Postal code |
8092 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE167484 |
Innate, translation-dependent silencing of an invasive transposon in Arabidopsis |
|
| Relations |
| BioSample |
SAMN18053592 |
| SRA |
SRX10166363 |
