|
| Status |
Public on Aug 24, 2015 |
| Title |
OsEZ1 |
| Sample type |
SRA |
| |
|
| Source name |
Root elongation zone
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Japonica
reference annotation used for mapping: Ensembl Release 19, MSU6
age: 4 days after plating
tissue: root
root zone: Root elongation zone
|
| Growth protocol |
Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones. RNA was extracted by Qiagen RNeasy Plant Mini Kit.
RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
8953
|
| Data processing |
Reads quality were checked by FastQC.
The first 15 bp of each read was trimmed to ensure high quality.
Reads were mapped to the mentioned reference annotation by Tophat2 with default setting.
Reads were quantified to RPKM by Cufflinks2 with default setting plus the correction for multi-read (-u)
Genome_build: see the reference that is listed in sample characteristics for each species.
Supplementary_files_format_and_content: A master tab-delimited text file (.csv) includes RPKM values of different development zones for each gene . There are two master sheets, one for gene expression of 3 development zones in 6 angiosperms, another for combined gene expression of elongation + differentiation zone in 7 vascular plants (6 angiosperms + selaginella).
|
| |
|
| Submission date |
Jan 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
John Schiefelbein |
| E-mail(s) |
schiefel@umich.edu
|
| Phone |
734-764-3580
|
| Organization name |
University of Michigan
|
| Department |
Molecular, Cellular, and Developmental Biology
|
| Street address |
830 North University Avenue
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL13160 |
| Series (1) |
| GSE64665 |
Conserved Molecular Program for Root Development in Diverse Plants |
|
| Relations |
| BioSample |
SAMN03275396 |
| SRA |
SRX828725 |
