|
| Status |
Public on Jan 26, 2018 |
| Title |
CS_120_r1 |
| Sample type |
SRA |
| |
|
| Source name |
CS_120_5d whole seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: VCS SOV (Col-0 [SOV-L.er])
time after transcription inhibition (min): 120
tissue: 5 d whole seedling
biological replicate no.: 1
|
| Treatment protocol |
Transcriptional arrest by vacuum infiltration. 50-60 seedlings per genotype per replicate treated in 3 mL 1 mM cordycepin with swirling.
|
| Growth protocol |
Seedlings were grown vertically on 0.5X MS growth media with 0.5% sucrose on 0.8% agar plates, at 22˚C, and in constant light for 5 d.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Omega Bio-Tek EZ RNA column extraction + Dnase I treatment
Plant RiboZero & Illumina TruSeq Stranded Kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FastQC was used to summarize read quality.
Bowtie2 version 2.2.3 & TopHat2 v2.0.12 were used to align reads to the genome yeilding BAM files.
samtools version 0.1.19-44428cd was used for indexing and sorting BAM files.
HTSeq 0.6.1 was used to summarize read counts by gene.
R version 3.1.0 was used to normalize read counts.
Genome_build: TAIR10
Supplementary_files_format_and_content: Library nomalized read counts (reads per million) are provided for each AGI gene identifier (rows) and for all 128 libraries (columns).
|
| |
|
| Submission date |
Sep 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Leslie Ellen Sieburth |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Utah
|
| Department |
Biology
|
| Street address |
257 South 1400 East
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84124 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE86359 |
The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings [RNA-seq] |
| GSE86361 |
The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings |
|
| Relations |
| BioSample |
SAMN05725432 |
| SRA |
SRX2095230 |
