|
| Status |
Public on Jul 18, 2017 |
| Title |
TruSeq ddm1 Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Inflorescence tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: ddm1
rna type: total RNA
library type: TruSeq
|
| Growth protocol |
Arabidopsis thaliana plants were grown on soil in a growth chamber at 22°C for two weeks in a 12h/12h light cycle and then transferred to a 16h/8h light cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from inflorescence tissue using the TRIzol extraction method.
To generate total RNA-seq libraries, RNA was subjected to ribodepletion with Ribo Zero (Illumina) and libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina). RNA 3’end libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) adjusted for longer insert lengths by diluting the second strand synthesis buffer with water in a ratio 1:1. sRNA-seq libraries were constructed by Fasteris SA. Libraries were prepared using the Illumina TruSeq Kit SBS v3.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ddm1_total2
TrueSeq_CPM.txt
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Trimming of reads with Trimmomatic-0-2.36 using the following parameters: SLIDINGWINDOW:4:10 AVGQUAL:20 MINLEN:50
Mapping to Arabidopsis genome (TAIR10) with STAR (--outFilterMultimapNmax 50 --outFilterMatchNmin 30 --alignSJoverhangMin 3 --alignIntronMax 10000)
Read counting with Rsubread (allowMultiOverlap=T, isPairedEnd=T, strandSpecific=2, countMultiMappingReads=T)
Read normalization with edgeR.
sRNA libraries were trimmed with Trimmomatic-0-2.36 using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15
sRNA counting was performed using the processReads-median.pl function of the ncPRO-seq v1.5.1 pipeline.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_CPM.txt: Tab-delimited text files of count per million (CPM) values.
Supplementary_files_format_and_content: met1_sRNA_processed.txt: Tab-delimited text file of counts per sRNA species.
|
| |
|
| Submission date |
Jan 13, 2017 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE93584 |
A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements |
|
| Relations |
| BioSample |
SAMN06227258 |
| SRA |
SRX2488470 |
