|
Status |
Public on Jun 08, 2017 |
Title |
Structure-seq2 Biotin variation (+DMS) Rep1 [Standard_primer_H] |
Sample type |
SRA |
|
|
Source name |
Shoot
|
Organism |
Oryza sativa Japonica Group |
Characteristics |
subspecies: japonica cultivar: Nipponbare tissue: shoot age: 14 days treatment: +DMS rt denaturation: 90 °C with salt rt reaction: 55 °C biotin added: yes rt purification: streptavidin ligation method: T4 DNA ligase ligation purification: streptavidin pcr enzyme: Q5 final purification: PAGE sequencing primer: standard
|
Treatment protocol |
See the 'characteristics' field.
|
Growth protocol |
Plants were germinated in a petri dish for 4-5 days, then transferred to potted soil for the remainder of 2 weeks.
|
Extracted molecule |
total RNA |
Extraction protocol |
Machery-Nagel NucleoSpin RNA Plant kit, and Thermo Fisher Scientific Poly(A) purist kit. Standard Structure-seq2 protocol. Briefly, reverse transcription was performed with SuperScript III, followed by ligation and PCR. Specifics are included in the 'characteristics' field.
|
|
|
Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
|
|
Description |
Standard_primer_H processed data file: All_info.xls
|
Data processing |
Library strategy: Structure-seq2 Trim 5' and 3' adapter using Cutadapt. Bowtie2 mapping to rice genome and cDNA library. Genome_build: ensemblgenomes_Oryza_sativa_release_31 Supplementary_files_format_and_content: All_info.xlsx: Raw read counts for each transcipt.
|
|
|
Submission date |
Feb 28, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Zhao SU |
Organization name |
The Penn State University
|
Department |
Biology
|
Lab |
Sarah Assmann
|
Street address |
354 N. Frear
|
City |
University Park |
State/province |
PA |
ZIP/Postal code |
16802 |
Country |
USA |
|
|
Platform ID |
GPL22703 |
Series (1) |
GSE95514 |
Structure-seq2: Sensitive and accurate genome-wide profiling of RNA structure in vivo |
|
Relations |
BioSample |
SAMN06471225 |
SRA |
SRX2599502 |