|
| Status |
Public on Apr 23, 2018 |
| Title |
mRNA-seq_C24/Col_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
seedling shoot
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 14 day old
ecotype: C24/Col
|
| Growth protocol |
Wild-type hybrid was generated by crossing Arabidopsis thaliana ecotype Col and C24. The shoots of 14-day-old seedlings were used for RNA-seq. All seedlings were grown under short-day condition (8 hours light at 22℃ and 16 hours dark at 18℃).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from shoots of 14-day-old Arabidopsis seedling using the Rneasy plant mini kit (Qiagen). mRNAs were extracted from the total RNAs by Dynabeads oligo(dT) (Invitrogen Dynal). First- and second-strand cDNAs were obtained using random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
polyA RNA isolated
|
| Data processing |
RNA-sequencing reads for Col and C24 were mapped to TAIR10 genome and C24 genome using Tophat software respectively. For hybrid RNA sequencing data analysis, we aligned the reads to both of the TAIR10 genome and C24 genome. Reads were assigned to an allele based upon the highest quality alignment and were further used to calculated allelic expression divergence.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for mRNA seq samples
|
| |
|
| Submission date |
Oct 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuncheng Wang |
| E-mail(s) |
[email protected]
|
| Organization name |
Peiking University
|
| Street address |
5 Yiheyuan Road
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL9062 |
| Series (1) |
| GSE62478 |
RNA-seq analysis of alternative splicing between two Arabidopsis accessions and its inheritance in hybrid |
|
| Relations |
| BioSample |
SAMN03121832 |
| SRA |
SRX737126 |
