|
Status |
Public on Jul 01, 2020 |
Title |
At.TRIzol.total.R1 |
Sample type |
SRA |
|
|
Source name |
At.inflorescence.TRIzol.total
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: inflorescence library preparation: TruSeq rna isolation: TRIzol molecule subtype: small RNA
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted with the standard TRIzol method or with the TRaPR isolation method. Libraries were prepared with from TRIzol or TRaPR isolated RNA with the TRUseq or Lexogen sRNA library preparation kits or with a custom library preparation protocol.
|
|
|
Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
processed data file: At_miRNA_counts.csv
|
Data processing |
Illumina Casava1.8 software used for basecalling. Trimming of reads with Trimmomatic 0.36 Mapping to the Arabidopsis thaliana genome (TAIR10) with Bowtie 1.2.1.1 Mapping to the Drosophila melanogaster genome (BDGP6) with Bowtie 1.2.1.1 Mapping to the Mus musculus genome (GRCm38) with Bowtie 1.2.1.1 Read counting to miRBase annotation with Rsubread 1.26.1 Read normalization with DEseq2. Genome_build: TAIR10 Genome_build: BDGP6 Genome_build: GRCm38 Supplementary_files_format_and_content: comma separated text files of library and log2 normalized miRNA read counts
|
|
|
Submission date |
Jul 18, 2019 |
Last update date |
Jul 01, 2020 |
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 |
GPL19580 |
Series (1) |
GSE134516 |
A universal, benchtop, gel-free method for the rapid and simultaneous isolation of all known classes of functional small RNAs |
|
Relations |
BioSample |
SAMN12317561 |
SRA |
SRX6470264 |