|
| Status |
Public on May 03, 2012 |
| Title |
Wild-type-3w replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
3-week-old wild type seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
condition: grown on soil
age: 3-week-old
ecotype: Columbia
rna fraction: polyA RNA
genotype/variation: wild type plants
|
| Growth protocol |
Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes containing LS agar (0.85%) medium supplemented with 1% sucrose for 2 weeks or on soil for 3 weeks under 16-h-light/8-h-dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the plants using Trizol reagent (Invitrogen, Carlsbad, CA). Poly(A)+ fraction was separated from 80 μg of total RNA using Oligotex mRNA Mini Kit (Qiagen, Valencia, CA) and fragmented using Fragmentation Reagents (Applied Biosystems/Ambion, Austin, TX) at 70°C for 15 min. Fifty nanograms of the fragmented RNA was used to generate strand-specific RNA-Seq library according to the Directional mRNA-Seq Library Preparation Protocol (Illumina). RNA-Seq libraries were sequenced for 42 cycles using the Illumina Genome Analyser II (wild type and fry1-6) or for 50 cycles using the HiSeq 2000 (xrn3-3, xrn3-3xrn4-6, 3-week-old wild type and xrn2-1xrn3-3) according to manufacturer’s instruction. Image analysis and base calling were performed with the standard Illumina pipeline. Read sequences were aligned with the Tophat software to the TAIR9 reference genome (Trapnell et al. 2009).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
biological replicate 2
|
| Data processing |
Read sequences were aligned with the Tophat software to the TAIR9 reference genome
|
| |
|
| Submission date |
Dec 22, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE34654 |
Genome-wide identification of non-coding RNAs targeted by XRN exoribonucleases in collaboration with FRY1 using RNA-Seq in Arabidopsis thaliana. |
|
| Relations |
| SRA |
SRX113697 |
| BioSample |
SAMN00769273 |
