|
| Status |
Public on Feb 01, 2022 |
| Title |
ERF096-RNAi cold stress rep3 |
| Sample type |
SRA |
| |
|
| Source name |
ERF096-RNAi
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
genotype: ERF096-RNAi
developmental stage: three leaf
tissue: leaf
|
| Treatment protocol |
The leaves of rice under normal growth conditions and those treated at 4°C for 12 h were quick-frozen in liquid nitrogen.
|
| Growth protocol |
Wild-type, OsERF096-OX and OsERF096-RNAi transgenic rice were grown in a culture room (14h day 10h night) to the three-leaf stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ERFiCTR3
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rice Annotation Project Database whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Rice Annotation Project Database
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Feb 01, 2022 |
| Last update date |
Feb 06, 2022 |
| Contact name |
Yang shen |
| E-mail(s) |
csmbl2016@126.com
|
| Phone |
+8615603692106
|
| Organization name |
Heilongjiang Bayi Agricultural University
|
| Lab |
Crop Stress Molecular Biology Laboratory
|
| Street address |
No. 5 Xinfeng Road, Longfeng District
|
| City |
Da qing |
| State/province |
Heilongjiang Province |
| ZIP/Postal code |
163319 |
| Country |
China |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE195853 |
Transcriptome differences between wild-type and ERF096 transgenic rice before and after cold treatment |
|
| Relations |
| BioSample |
SAMN25538084 |
| SRA |
SRX14004174 |
