|
| Status |
Public on Jan 14, 2013 |
| Title |
mRNA from Arabidopsis Col-0 hae-3 hsl2-3 stage 15 flower receptacles 2 |
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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_2.bed: TAIR10
h3h3_2_count.txt: TAIR10
|
| |
|
| 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 |
SRX117109 |
| BioSample |
SAMN00778816 |
