|
| Status |
Public on Jun 06, 2019 |
| Title |
AGO1IP_10G1_rep5 |
| Sample type |
SRA |
| |
|
| Source name |
BY-2 cell suspension, G1 phase, AGO1 IP
|
| Organism |
Nicotiana tabacum |
| Characteristics |
cell line: Tobacco BY-2
expression: GFP-fused AGO1
growth type: suspension
cell cycle phase: G1
rip antibody: VHH anti-GFP (Chromotek, Ref: gtm-20)
replicate: 5
|
| Treatment protocol |
Cells were synchronized using aphidicolin 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 were kept in the dark, on a shaker 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.
Small RNA libraries were constructed following Illumina TruSeq Small RNA Library Preparation Kit.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Small RNA-seq
AGO1 IP RNA
|
| Data processing |
For these small RNA libraries, raw files resulting from 2 separate runs were processed and concatenated to produce a single processed file.
Read quality control using FastQC.
Adaptor trimming and chopping using Trimmomatic.
Genome alignment using Bowtie and TN90 Nicotiana tabacum genome.
Sequences are then formatted to tag-count format.
Genome_build: N. tabacum TN90 (Sierro et al. 2014)
Supplementary_files_format_and_content: *_chopped.txt: Tab-delimited text files; Final trimmed and cropped output file in tag-count format.
|
| |
|
| Submission date |
Aug 07, 2017 |
| Last update date |
Jun 06, 2019 |
| Contact name |
Patricia Baldrich Gonzalez |
| E-mail(s) |
pbaldrich@ucdavis.edu
|
| Organization name |
University of California - Davis
|
| Department |
Meyers Lab
|
| 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 |
GPL22345 |
| Series (2) |
| GSE102341 |
Cell cycle dependent regulation and function of Argonaute 1 in plants [small RNA-seq] |
| GSE102344 |
Cell cycle dependent regulation and function of Argonaute 1 in plants |
|
| Relations |
| BioSample |
SAMN07457647 |
| SRA |
SRX3069198 |
