|
| Status |
Public on Jun 06, 2019 |
| Title |
totalRNA_1S_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cell suspension
|
| Organism |
Nicotiana tabacum |
| Characteristics |
cell line: BY-2
cell cycle phase: S
replicate: 1
|
| Treatment protocol |
Cells were synchronized following the published protocol from Nagata et al 1992.
|
| Growth protocol |
Cells were weekly subcultured in liquid MS medium supplemented with KH2PO4 (200mg/L), myo-inositol (100mg/L), thiamin (1mg/L), 2,4-D(0,2mg/L) and sucrose ( 30g/L). Cells are kept in the dark, on a shacker at 180 RPM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were vacuum filtered and frozen in liquid nitrogen. After mechanical grinding, RNA was extracted using Trizol/chloroform protocol.
RNA libraries were constructed following Illumina TruSeq Stranded mRNA Library Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Cells were synchonized using aphidicolin
|
| Data processing |
For these RNA libraries, raw files resulting from 2 separate runs were processed and concatenated to produce a single processed file
Read quality control usinf FastQC
Adaptor trimming and chopping using Trimmomatic
Genome alignment unig HiSat2 and TN90 Nicotiana tabacum genome
sequeces are then formated to tag-count format
Genome_build: Nicotiana tabacum genome version 4 (Edwards et al., 2017)
Supplementary_files_format_and_content: Final trimmed and cropped output file in tag-count format
|
| |
|
| Submission date |
Oct 09, 2018 |
| Last update date |
Jun 06, 2019 |
| Contact name |
Patricia Baldrich Gonzalez |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California - Davis
|
| Department |
Genome Center
|
| Lab |
Meyers Lab
|
| Street address |
451 Health Sciences Dr., Davis, CA 95616
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL25653 |
| Series (2) |
| GSE102344 |
Cell cycle dependent regulation and function of Argonaute 1 in plants |
| GSE121032 |
Cell cycle dependent regulation and function of Argonaute 1 in plants [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN10227712 |
| SRA |
SRX4823668 |
