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Sample GSM7901043 Query DataSets for GSM7901043
Status Public on Apr 04, 2024
Title Col-0_nuc_FC1_rep4
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 SAMN38264828
SRA SRX22532946

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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