|
| Status |
Public on Dec 14, 2024 |
| Title |
RNA seq, Apoplastic washing fluid, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Leaf
genotype: Columbia 0
|
| Growth protocol |
Arabidopsis thaliana Col-0 seeds were grown in a temperature-controlled room under a 9 h light/15 h dark photoperiod with 150 μmol ms photosynthetic photon fl ux density.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total leaf RNA (cell lysate) was extracted from 100 mg of leaf tissue using TRIzol Reagent (Thermo Fisher Scientifi c™, Waltham, MA)
sRNA libraries were constructed using the RealSeq-AC kit version 2 (Realseq Biosciences, Santa Cruz, CA, catalog no. 500-00048;) as per the manufacturer’s instructions. For RNAseq libraries, we used NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, catalog no. E7760L) protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Library name: RNAseq_AWF_R2
|
| Data processing |
We sent all sRNA and RNAseq libraries for sequencing to the University of Delaware Sequencing and Genotyping Center, where they were sequenced on a NovaSeq2000 instrument using 50-bp single-end reads for sRNA and 75-bp paired-end reads for RNAseq.
For sRNA libraries we first trimmed the adaptors using Cutadapt version 1.16 using a minimum insert size of 10 nt and no maximum. We assessed sequence quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/ fastqc/). We aligned clean reads to the Arabidopsis genome (TAIR version 10) and all subsequent analyses were performed using the software Bowtie2. For miRNA analyses, we used the latest version of miRBase (version 22).
For RNA-seq libraries were analyzed using HiSat2 and Stringtie pipeline, and the TAIR10 available annotation file.
Assembly: Arabidopsis genome (TAIR version 10)
Supplementary files format and content: small RNA seq.: microRNA count files
Supplementary files format and content: RNAseq.: gtf count files
|
| |
|
| Submission date |
Dec 10, 2024 |
| Last update date |
Dec 14, 2024 |
| Contact name |
Patricia Baldrich Gonzalez |
| E-mail(s) |
pbaldrich@ucdavis.edu
|
| Organization name |
University of California - Davis
|
| Department |
Genome Center
|
| Street address |
451 Health Sciences Dr., Davis, CA 95616
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL30821 |
| Series (1) |
| GSE283977 |
Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs |
|
| Relations |
| BioSample |
SAMN45496293 |
| SRA |
SRX27031194 |
