|
| Status |
Public on Aug 26, 2013 |
| Title |
suvr5-1 |
| Sample type |
SRA |
| |
|
| Source name |
suvr5-1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
genetic variant: suvr5-1
tissue: leaves
|
| Growth protocol |
All plants were grown under long day conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaves from wild type Col-0, suvr5-1, ldl1-2 ldl2 and suvr5-1 ldl1-2 ldl2 3 week-old plants were used for RNA extraction using Trizol (Invitrogen) following the manufacturer instructions. 10 mg of total RNA was treated with DNaseI (Roche), and cleaned up with RNeasy columns (Qiagen). Poly(A) was purified using the Dynabeads mRNA Purification Kit (Invitrogen) and used to generate the mRNA-seq libraries following the manufacturer’s instructions (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
mRNA-Seq reads were first trimmed to 50mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads.
Genome_build: TAIR8
Supplementary_files_format_and_content: Processed files indicate the coordinates of uniquely mapped reads. Column 1 is chromosome. Column 2 is the genomic strand (+/-). Column 3 is the genomic coordinate.
|
| |
|
| Submission date |
Jul 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Hume Stroud |
| Organization name |
UT Southwestern
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE39405 |
The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner |
| GSE58029 |
The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN01090431 |
| SRA |
SRX573003 |
