|
Status |
Public on Feb 01, 2022 |
Title |
ERF096-RNAi CK rep2 |
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 |
ERFiCKR2
|
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 |
SAMN25538094 |
SRA |
SRX14004164 |