|
| Status |
Public on Apr 01, 2023 |
| Title |
circular RNA 180640A&B_Sham-3 |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Rattus norvegicus |
| Characteristics |
time: 0 h after modeling
tissue: blood
|
| Growth protocol |
Sprague-Dawley (SD) male rats, weighing 250 to 300 g and 6 to 8 weeks in age, were fed conventionally. Animal feeding environment: 12 hours of day and night alternately, constant humidity (50 ± 5)%, temperature 20 ~ 25 ℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood were collected in PAXgene blood RNA tube, stored in -80℃, and RNA was harvested using PAXgene method. NEBNext Ultra RNA Library Prep Kit for Illumina (Cat#E75305) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Pair end 150bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sham-3
|
| 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 Rnor_6.0 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: Rnor_6.0
|
| |
|
| Submission date |
Apr 08, 2020 |
| Last update date |
Apr 01, 2023 |
| Contact name |
baolan sun |
| E-mail(s) |
dwf@ntu.edu.cn
|
| Organization name |
Affiliated Hospital of Nantong University
|
| Street address |
20 Xisi Road
|
| City |
Nantong |
| ZIP/Postal code |
226001 |
| Country |
China |
| |
|
| Platform ID |
GPL14844 |
| Series (2) |
| GSE148332 |
Expression and Possible Mechanism of circular RNA rno_CIRCpedia_1953 in Deep Venous Thrombosis (circular RNA) |
| GSE148333 |
Expression and Possible Mechanism of circular RNA rno_CIRCpedia_1953 in Deep Venous Thrombosis |
|
| Relations |
| BioSample |
SAMN14560299 |
| SRA |
SRX8083152 |
