|
| Status |
Public on Jun 08, 2017 |
| Title |
Low RT denaturationTemp. [Custom_primer_L] |
| 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: 65 °C without salt
rt reaction: 55 °C
biotin added: no
rt purification: PAGE
ligation method: T4 DNA ligase
ligation purification: PAGE
pcr enzyme: Q5
final purification: PAGE
sequencing primer: custom
|
| 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 |
Custom_primer_L
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 |
SAMN06471268 |
| SRA |
SRX2599519 |
