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Status |
Public on Jan 14, 2013 |
Title |
mRNA from Arabidopsis Col-0 hae-3 hsl2-3 stage 15 flower receptacles 1 |
Sample type |
SRA |
|
|
Source name |
Stage 15 flower receptacles hae-3 hsl2-3 mutant
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Col-0 genotype/variation: hae-3 hsl2-3 mutant tissue: Flower Receptacles, from base of flower to slightly above attachment point of floral organs, including petal, sepal, and stamen tissue in between. developmental stage: Stage 15 Flowers
|
Growth protocol |
Plants were grown in 16h light 8h dark at 22C
|
Extracted molecule |
total RNA |
Extraction protocol |
Libraries were constructed from mRNA using the Illumina TruSeq RNA sample preparation kit (#RS-930-2001) following manufactuer's protocols.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Reads were trimmed for quality using Fastx fastq quality trimmer with a min quality score of 13 and a min length of 32 bps. Reads were then trimmed for adaptor sequence from the 3' end using CUTADAPT with a overlap of 2bp and a min length of 32 bp. Trimmed reads were then aligned to the Arabidopsis TAIR10 genome using TOPHAT v 1.3.1 using standard settings. Reads were summed for each gene using HTseq-count and differential expression tested using DESeq v 1.5.6. Genome Build: h3h3_1.bed: TAIR10 h3h3_1_count.txt: TAIR10
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Submission date |
Jan 24, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Chad E. Niederhuth |
Organization name |
Michigan State University
|
Department |
Plant Biology
|
Street address |
612 Wilson Road
|
City |
East Lansing |
State/province |
M |
ZIP/Postal code |
48824 |
Country |
USA |
|
|
Platform ID |
GPL13222 |
Series (1) |
GSE35288 |
Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq |
|
Relations |
SRA |
SRX117108 |
BioSample |
SAMN00778815 |