|
Status |
Public on Aug 08, 2021 |
Title |
ddm1_total_SMARTseq_1 |
Sample type |
SRA |
|
|
Source name |
inflorescence
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: inflorescence genotype: ddm1 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 |
SAMN18511125 |
SRA |
SRX10458491 |