|
| Status |
Public on Dec 21, 2014 |
| Title |
Col_MS_RNASeq_Rep#2 |
| Sample type |
SRA |
| |
|
| Source name |
Etiolated seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
growth stage: 3-d old
ecotype: Col-0
genotype/variation: wild type
growth medium: MS medium
|
| Treatment protocol |
Kynurenine treatment for Sample K1 and K3 were directly supplied to the growth medium
|
| Growth protocol |
Surface-sterilized seeds were sown on respective medium and imbibed at 4°C for 3d. Plates were kept under light for 3~4h after imbibition to promote seed germination, wrapped with aluminum foil, and incubated in the dark at 22°C for 3d.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3-day-old etiolated seedlings of different samples were frozen and grinded in liquid nitrogen. Total RNA was extracted by RNeasy Plant Mini Kit (QIAGEN) from the samples, then the mRNA was fragmented into short fragments (about 350 bp) by the fragmentation buffer and converted into double-stranded cDNA by random hexamer-primer using the mRNA fragments as templates and buffer, dNTPs, RNase H and DNA polymerase I treatment. The double strand cDNA was purified with QiaQuick PCR extraction kit. Finally, sequencing adaptors were ligated to the fragments. The adaptor-ligated DNA fragments in right size were selected and purified by electrophoretic gel and enriched by PCR amplification(16 cycles). The PCR products were purified using PCR purification kit (Qiagen), and the insert size and DNA concentration were determined by bioanalyzer (Agilent) to get the final seq-library for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA sequencing of Col seedling grown on MS, biological repeat 2
|
| Data processing |
The original image data generated by sequencing machine were transferred into sequence data via base calling (Illumina Pipeline v1.3.1.) and were subjected to quality control (QC). Then raw reads were filtered into clean reads, TopHat (version 1.3.0) was used to align the reads to the Arabidopsis thaliana (TAIR10). The gene expression level was calculated by using RPKM method.
|
| |
|
| Submission date |
Sep 18, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Hongwei Guo |
| E-mail(s) |
hongweig@pku.edu.cn
|
| Phone |
86-10-62767823
|
| Fax |
86-10-62751526
|
| Organization name |
Peking University
|
| Department |
College of Life Sciences
|
| Lab |
Guo Lab
|
| Street address |
No.5 Yiheyuan Road
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE32202 |
Expression profiles of IAA biosynthesis deficient seedlings of Arabidopsis thaliana |
|
| Relations |
| SRA |
SRX097601 |
| BioSample |
SAMN00718913 |
