|
| Status |
Public on Oct 22, 2012 |
| Title |
PTB_OE2_R1 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype: At5g53180 overexpression
developmental stage: 11 days old seedlings
|
| Growth protocol |
Arabidopsis seeds were surface sterilized and plated on 1/2 MS medium containing 2% sucrose and 0.8% phytoagar. Following stratification for 2 days in darkness at 4°C plates were transferred to continuous light (~20°C, ~60% humidity). Seedlings were sampled after cultivation for 11 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from ∼100 mg of plant tissue using the Universal RNA Purification kit (EURx), including an on-column DNaseI treatment performed according to the manufacturer's instructions.
Libraries were prepared using the Illumina TruseqTM sample prep kit (Illumina) according to the manufacturer's instructions (TruSeqTM RNA Sample Preparation v2 Guide, version: November 2010). For the adapter ligation step, the RNA Adapter Indexes 10 (AR010) and 13 (AR013) were used. Following the PCR enrichment step using half the sample volume, libraries were subjected to an additional gel purification step. A size range of 250-350 bp was extracted from a 2% agarose gel and purified using the MinElute Gel Extraction Kit (Qiagen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
429 R1 (oe_2)
|
| Data processing |
Illumina Raw Data processing with SHORE 4.1 pipeline with application 'mRNA' and disabled Illumina filter
fastq files were aligned to the TAIR10 reference 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) MI12; (4) MI3; (5) OE1; (6) OE2; (7) OE3
|
| |
|
| 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) |
| GSE41433 |
Polypyrimidine tract-binding protein homologues from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes |
|
| Relations |
| SRA |
SRX193195 |
| BioSample |
SAMN01760500 |
