|
| Status |
Public on Dec 01, 2012 |
| Title |
nrpe1 RNA replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
2-3 week seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: nrpe1
|
| Growth protocol |
Strains were grown under long day conditions for 2-3 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Plant Mini Kit (Qiagen). rRNA depletion was performed using the RiboMinus Plant Kit (Invitrogen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Image analysis and base calling were performed using standard illumina pipelines.
RNA-Seq reads were aligned via the Tophat software.
Differential transcripts between wild-type and mutants were called by Cufflinks using TAIR10 annotations of genes and transposons.
Genome_build: TAIR10
Supplementary_files_format_and_content: csv with list of gene differentially expressed in nrpe1, swi3b, and idn2 compared to Col0
|
| |
|
| Submission date |
Jun 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
M Jordan Rowley |
| E-mail(s) |
jordan.rowley@unmc.edu, jordrow@gmail.com
|
| Phone |
7343580454
|
| Organization name |
Univ of Nebraska Medical Center
|
| Department |
GCBA
|
| Lab |
Rowley
|
| Street address |
601 S Saddle Creek Rd
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68106 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE38400 |
A SWI/SNF nucleosome remodeling complex acts in non-coding RNA-mediated transcriptional silencing |
| GSE38464 |
Nucleosome remodeling by the SWI/SNF complex in non-coding RNA-mediated transcriptional gene silencing |
|
| Relations |
| SRA |
SRX151568 |
| BioSample |
SAMN01036862 |
