|
| Status |
Public on Oct 12, 2014 |
| Title |
rice_rep4_sec3 |
| Sample type |
SRA |
| |
|
| Source name |
rice leaf section 3
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Nipponbare
tissue: leaf
leaf section: 3
age: 14 days
|
| Treatment protocol |
Nine day old third leaves of maize were cut into fifteen 1 cm segments; samples were pooled from an average of seven plants per biological replicate and six biological replicates in total were collected on different dates. 14 day old third leaves of rice were cut into eleven 2 cm segments, samples were pooled from an average of 15 plants per biological replicate and four replicates in total were collected.
|
| Growth protocol |
The seedlings were grown under an 80:20 mix of metal halide, with capsylite halogen lamps at light intensity of 550 μmol/m2/sec, 12:12 l/D, 31 °C L/22 °C D and 50% relative humidity.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol (Invitrogen, CA) following manufactory’s suggestion.
The libraries were constucted following the protocol described in the article: Wang, L. et al. A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq. PloS one 6, e26426 (2011).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
leaf section 3, replicate 4
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the reference genome using the software Tophat v2.0.10.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff ( v2.1.1).
Genome_build: MSU_osa1r7
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each Sample.
|
| |
|
| Submission date |
Jan 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Timothy Nelson |
| Organization name |
Yale University
|
| Department |
Department of Molecular, Cellular and Developmental Biology
|
| Street address |
PO Box 208104
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520-8104 |
| Country |
USA |
| |
|
| Platform ID |
GPL13160 |
| Series (1) |
| GSE54274 |
Exploring the mechanism of C4 photosynthetic differentiation through a unified comparative analysis of maize and rice leaf transcriptomes |
|
| Relations |
| BioSample |
SAMN02594289 |
| SRA |
SRX445715 |
