|
| Status |
Public on Dec 15, 2013 |
| Title |
WT_mRNA_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
3 wk leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
age: 3 weeks
tissue: leaves
|
| Growth protocol |
Plants were grown under continuous light
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA-seq: RNA-seq experiments were performed in two biological replicates for each genotype. Tissue was ground in Trizol (Invitrogen). Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina Truseq).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
mRNA-seq: Reads were mapped using Bowtie (Langmead et al., 2009) allowing up to 2 mismatches, and uniquely mapping reads were retained.
supplementary_files_format_and_content: mRNA-seq: Wiggle format files with normalized read densities calculated in 25 bp bins. Normalized reads were calculated by # reads/0.1kb/uniquely mapping readsx10^6.
Genome_build: TAIR10
|
| |
|
| Submission date |
Sep 30, 2013 |
| 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 (1) |
| GSE51304 |
Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis |
|
| Relations |
| BioSample |
SAMN02370195 |
| SRA |
SRX361908 |
