|
|
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|