|
| Status |
Public on Oct 01, 2013 |
| Title |
NMD_CHX_R1 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype: wild type
developmental stage: 11 days old seedlings
treatment: incubated for 4 h in liquid MS medium containing 10 µg/ml cycloheximide
|
| Growth protocol |
seedlings were grown on 1/2 MS medium containing 2% sucrose for 11 days under continuous light conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
seedlings were ground in liquid N2 and total RNA was isolated using the Universal RNA purification kit (Roboklon)
Libraries were prepared using the Illumina TruSeq™ sample prep kit starting from 2-4 µg of total RNA and following the instruction manual (TruSeq RNA Sample Preparation v2 Guide; November 2010)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Col-0 t=4h CHX #1
|
| Data processing |
Illumina Raw Data processing with SHORE 4.1 pipeline with application 'mRNA' and disabled illumina filter
Fastq file were aligned to the TAIR10 genome with the spliced aligner PALMapper (version 4)
Alignment postprocessing (filtering and multimapper resolution) using RNAgeeq
Reads were counted as overlapping to a gene, if they shared at least one exonic position
Expression values were transformed to RPKM (Reads per kilobase per million mapped reads)
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text-file, with following columns: (1) gene id; (2) WT; (3) UPF1; (4) UPF3; (5) UPF1UPF3; (6) MOCK; (7) CHX
|
| |
|
| Submission date |
Oct 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Andre Kahles |
| E-mail(s) |
akahles@cbio.mskcc.org
|
| Organization name |
Memorial Sloan-Kettering Cancer Center
|
| Department |
Computational Biology Center
|
| Lab |
Rätsch Lab
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE41432 |
Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the eukaryotic steady state transcriptome |
|
| Relations |
| SRA |
SRX193185 |
| BioSample |
SAMN01760490 |
