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Sample GSM797874 Query DataSets for GSM797874
Status Public on Dec 21, 2014
Title wei8tar2_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: wei8-/- tar2+/-
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 wei8tar2(+/-) 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 SRX097605
BioSample SAMN00718917

Supplementary file Size Download File type/resource
GSM797874.txt.gz 396.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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