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Sample GSM994839

Query DataSets for GSM994839

Status

Public on Sep 01, 2013

Title

35S:SsCBF1-11

Sample type

SRA

Source name

Aerial part

Organism

Arabidopsis thaliana

Characteristics

developmental stage: 4-week-old seedlings
number of plants: 20 seedlings
genotype: SsCBF1-overexpressing line
cultivar: Col-0

Growth protocol

Seedlings of 35S:SsCBF1-11 and Col-0 (WT) plants were grown in a chamber at 22 ℃ in a photoperiod of 16 h light and 8 h darkness.

Extracted molecule

total RNA

Extraction protocol

Materials from 20 plants of each genotype were pooled for RNA isolation.Total RNA was isolated with Trizol reagent ( Invitrogen , USA ) from the aerial part of our material and purified with Micropoly(A) PuristTM mRNA purification kit (Ambion, USA, Cat. No:1919). About 10 μg total RNA of each sample was used for the construction of sequencing libraries. cDNA first- and second-strand synthesis was performed using Superscript II reverse transcriptase (Invitrogen,USA) and Ex Taq polymerase (TaKaRa, Japan), respectively.The newly synthesized double-strand cDNA was fractured into 300-500bp fragments using an ultrasonic instrument (Fisher) and then purified with AMPure beads ( Agencourt , USA ). The sequencing library was prepared and PCR amplified using TruSeqTM DNA Sample Prep Kit-Set A (illumina, USA) and TruSeq PE Cluster Kit (illumina, USA), respectively. Sequencing was performed on the illumina HiSeq 2000 sequencing platform.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Illumina Casava version 1.7 software was used for basecalling
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using a protocol from Mortazavi et al., Nature, 2008
MARS (MA-plot-based method with Random Sampling model) from DEGseq package was used for identifying differentially expressed genes (Wang et al., 2010)
Pathways and Gene Ontology (GO) analysis were performed using Molecule Annotation System (MAS)
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample and Pathway and Gene Ontology analysis of differentially expressed genes

Submission date

Aug 30, 2012

Last update date

May 15, 2019

Contact name

Lili Zhang

Organization name

Northeast Agricultural University

Street address

Mucai street

City

Harbin