|
| Status |
Public on May 01, 2017 |
| Title |
SCL28-OX_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
SCL28 overexpression
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: SCL28-OX #10
age: 5 d-old
tissue: root tip
|
| Growth protocol |
Plant seedlings were grown on 1/2 MS agar plates under a constant light condition at 22 ℃ in a growth room
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were extracted from roots of 5 d-old seedlings using TRI REAGENT (Molecular Research Center, USA) according to the manufacturer’s instructions. The samples were cleaned up with RNeasy Plant Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
Libraries were prepared using Truseq Stranded mRNA Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
OX-2
|
| Data processing |
Base-calling was performed using CASAVA (Version 1.8.2)
Reads were mapped using Tophat v2.0.13 based on the reference sequences
gtf file (annotation file) for each sample was produced using cufflink v2.2.0. Each file was merged by cuffmerge and quantification for each sample was performed using cuffquant.
Abundant calculation (FPKM) were perfomed using cuffdiff v2.2.0.
Genome_build: TAIR10
Supplementary_files_format_and_content: The excel file include matrix tables containing FPKM values for each sample and each sample group
|
| |
|
| Submission date |
Mar 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeong-eun Choe |
| E-mail(s) |
bioje14@konkuk.ac.kr
|
| Organization name |
Konkuk University
|
| Street address |
120 Neungdong-ro
|
| City |
Seoul |
| ZIP/Postal code |
05029 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE96945 |
RNA-seq analysis of WT and SCL28-OX in the Arabidopsis thaliana root tip |
|
| Relations |
| BioSample |
SAMN06629486 |
| SRA |
SRX2662877 |
