|
| Status |
Public on Apr 04, 2024 |
| Title |
Col-0_nuc_FC1_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
rosette
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: rosette
age: 14d
sequencing run: FlowCell1
genotype: Col-0
compartment: nucleus
|
| Growth protocol |
Seeds of Arabidopsis thaliana (Col-0) were stratified in darkness for 48 h at 4°C and plants were grown and propagated at 21°C on soil in a phytochamber or on MS medium in plant incubators (PolyKlima) under long-day conditions (16h light at 21°C and 8h darkness at 18°C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclear and cytoplasmic fractions were prepared from rosettes of 14-d plants adapting a previously described protocol based on differential centrifugation (Park et al., 2005). RNA was isolated from nuclear and cytoplasmic fractions using the RNeasy Plant Mini Kit (Qiagen). Additionally, the ERCC RNA Spike-In Mix (ambion) was added
RNA-seq libraries were prepared using NuGEN Universal Plus RNA-Seq with NuQuant User Guide v3 (Tecan Genomics) in combination with Arabidopsis rRNA AnyDeplete module
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
UMIs in header
|
| Data processing |
Reads were mapped to the TAIR10 genome (Lamesch et al., 2012) and ERCC sequences using STAR (v2.7.8a, ‘--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --outFilterMismatchNoverReadLmax 0.04 --outSAMmultNmax 1 –outMultimapperOrder Random’).
After tagging duplicated sequences using Picard MarkDuplicates (v2.21.8) (https://broadinstitute.github.io/picard/) the UMIs were used to remove technical duplicates using umi_tools dedup (v1.0.1).
For the differential gene expression analysis, the resulting reads from the pipeline outlined above were used to create a count table using the featureCounts function of the rsubread package (v1.6.3) (Liao et al., 2019)
Code is available at GitHub (uschwartz/mos11)
Assembly: TAIR10
Supplementary files format and content: tab delimited text file includes raw counts for each sample after merging samples on different flow cells
|
| |
|
| Submission date |
Nov 15, 2023 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Uwe Schwartz |
| E-mail(s) |
uwe.schwartz@ur.de
|
| Organization name |
University of Regensburg
|
| Department |
NGS Analysis Center
|
| Street address |
Universitätstraße 32
|
| City |
Regensburg |
| ZIP/Postal code |
93053 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30821 |
| Series (1) |
| GSE247811 |
Arabidopsis mRNA export factor MOS11: molecular interactions and role in abiotic stress responses |
|
| Relations |
| BioSample |
SAMN38264829 |
| SRA |
SRX22532945 |
