|
| Status |
Public on Jul 18, 2011 |
| Title |
Ler x Col endosperm RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
endosperm 6-7 days after pollination
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genetic background: Ler female X Col-0 male
tissue: endosperm
age: 6-7 days after pollination
|
| Growth protocol |
Plants were grown on soil in 16h days at 22 C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Seeds (600-1000) from crosses between multiple individuals were hand-dissected and total embryo or endosperm RNA isolated using the Ambion RNaqueous Kit with Plant RNA Isolation Aid. LIbraries were constructed using the Illumina mRNA-seq kit and protocol. 1 microgram of total RNA was poly-A selected twice, fragmented, and converted into double-stranded cDNA. The cDNA was end-repaired, adenylated, and adapters ligated. Adapter-ligated DNA approximately 200 bp in length was gel purified and amplified using Illumina PCR primers PE1.0 and PE2.0 with 15 amplification cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
mRNA-seq
|
| Data processing |
Sequencing reads were aligned to the TAIR 9.0 version of the Arabidopsis reference genome (www.arabidopsis.org) using the TopHat read aligner (http://tophat.cbcb.umd.edu/). Low quality reads and reads that mapped to more than one position in the genome with the same alignment score were discarded. Reads that mapped to more than one gene due to overlapping exons were not considered in further analyses. SAM files for each sequencing run of the same library are deposited separately.
|
| |
|
| Submission date |
Jul 08, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Mary Gehring |
| Organization name |
Whitehead Institute for Biomedical Research
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE30511 |
Allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col and Ler reciprocal F1 hybrid embryo and endosperm |
|
| Relations |
| SRA |
SRX082189 |
| BioSample |
SAMN00632352 |
