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Sample GSM1248695 Query DataSets for GSM1248695
Status Public on May 31, 2015
Title ColxC24_ZT0_mRNAseq
Sample type SRA
 
Source name Rosette leaves
Organism Arabidopsis thaliana
Characteristics genotype: F1 hybrid between Col and C24 with Col as the maternal parent
time point (zt time): ZT0
Stage: Before bolting
age: 3 weeks old
Growth protocol All plants were grown on soil under a 16/8-hour light/dark cycle with temperatures of 22C (light) and 20C (dark).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from mature leaves (3 week old A. thaliana) prior to bolting using plant RNA purification reagent (Invitrogen, Carlsbad, CA). The integrity of extracted RNA was verified by resolving 1ug RNA in an 1% formaldehyde denaturing agarose gel. An aliquot of 10ug total RNA was used to prepare mRNA-seq libraries using Illumina mRNA-seq sample preparation kit (Illumina Inc., San Diego, CA). Libraries with a range of 200-25 bp were excised and amplified for subsequent cluster generation and massively parallel sequencing using the Illumina Genome Analyzer with read lengths of 84 bp.
mRNA libraries were prepared for sequencing using standard Illumina kit protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
 
Data processing Alignment: mRNA-seq reads each were mapped to the TAIR9 genome and cDNA sequence using BFAST software (http://bfast.sourceforge.net)
RPKM values were calculated using a previously published method (Shi, X., Ng, D.W.-K., Zhang, C., Comai, L., Ye, W. and Chen, J.Z. (2012) Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids. Nat. Commun. 3, 950.)
Genome_build: TAIR9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. FIELD #1: AGI number; #2: RPKM
 
Submission date Oct 23, 2013
Last update date May 15, 2019
Contact name Z Jeffrey Jeffrey Chen
E-mail(s) zjchen@austin.utexas.edu
Phone 512-475-9327
Organization name The University of Texas at Austin
Department Molecular Biosciences
Lab Polyploidy, Hybrid Vigor, and Epigenetics
Street address 2506 Speedway NMS 3.122 Stop A500
City Austin
State/province TX
ZIP/Postal code 78712-1597
Country USA
 
Platform ID GPL9062
Series (1)
GSE51578 Natural Variation and Timing of Stress Responses Promote and Predict Heterosis
Relations
BioSample SAMN02380915
SRA SRX366975

Supplementary file Size Download File type/resource
GSM1248695_RPKM_ColxC24_ZT0.txt.gz 220.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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