|
| Status |
Public on May 26, 2012 |
| Title |
Col_mRNA_leaves |
| Sample type |
SRA |
| |
|
| Source name |
WT (eco Columbia) leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia-0
genotype/variation: WT
tissue: 3 week old leaves
|
| Growth protocol |
Constant light
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina TruSeq mRNA protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Col library
|
| Data processing |
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using Bowtie short read aligner. Alignments allowed for 2 mismatches and only uniquely mapping reads were retained for further analysis. The nrpe1, idn2, and idn2 idnl1 idnl2 libraries were compared to the Col library, and the idnl1 idnl2 library, which was sequenced separately with the Col_2 library, was compared to the Col_2 libary.
Genome Build:
Col_leaves_RPKM_TAIR8_values.txt: TAIR8
Processed data files report RPKM values.
|
| |
|
| Submission date |
Feb 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Joel Hale |
| E-mail(s) |
chris.joel.hale@gmail.com
|
| Organization name |
University of Washington
|
| Department |
Pathology
|
| Lab |
Center for Precision Diagnostics
|
| Street address |
1959 NE Pacific St., HSC H-458
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE36129 |
An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [leaves RNA-seq] |
| GSE36148 |
An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis |
|
| Relations |
| SRA |
SRX123429 |
| BioSample |
SAMN00792937 |
