|
| 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 |
