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Sample GSM5213534 Query DataSets for GSM5213534
Status Public on Aug 08, 2021
Title col0_total_SMARTseq_1
Sample type SRA
 
Source name inflorescence
Organism Arabidopsis thaliana
Characteristics tissue: inflorescence
genotype: wildtype (col0)
rna isolation: TRIzol
library preparation: SMART-seq2
Extracted molecule total RNA
Extraction protocol RNA was extracted with the standard TRIzol method.
NanoPARE and SMART-seq2 mRNA library preparation was performed as previously reported. cDNA was tagmented using the Illumina Nextera DNA library preparation kit, purified using the Zymo 5× DNAClean and Concentrator kit (ZymoResearch) and eluted with nuclease-free water. For final enrichment PCR, the purified reaction was split and amplified either with Tn5.1/TSO enrichment oligonucleotide or Tn5.2/TSO enrichment oligonucleotide primer sets. PCR reaction products with Tn5.1/TSO enrichment oligonucleotide and Tn5.2/TSO enrichment oligonucleotide primer sets were pooled and purified using AMPureXP DNA beads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description mRNA-seq
gene_TPM_SMARTseq2.csv
consensus_features.bed
Data processing nanoPARE Analysis Tools
Read trimming - Cutadapt
Read mapping - STAR
5p-end calssifcation and quantification - EndGraph
Genome_build: TAIR10
Supplementary_files_format_and_content: TPM
 
Submission date Mar 26, 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 SAMN18510985
SRA SRX10458489

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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