|
| Status |
Public on Jun 22, 2020 |
| Title |
lncRNA T_6W_1 |
| Sample type |
SRA |
| |
|
| Source name |
thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: thymus
age: 6-week-old
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The thymuses harvested from each group were placed in cryopreservation tubes and immediately immersed in liquid nitrogen (−196°C) for preservation.Total RNA from each thymus sample was isolated using the TRIzol Reagent kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
lncRNA.expression.txt
mRNA.expression.txt
circRNA.expression.txt
|
| 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 mm8 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: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...
|
| |
|
| Submission date |
Oct 31, 2019 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Wen Ting Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Shenzhen PKU-HKUST Medical Center
|
| Street address |
No,1120,LianHua Road,FuTian District
|
| City |
Shenzhen |
| ZIP/Postal code |
518000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE139653 |
Comprehensive analysis of circRNA expression profiles and circRNA-associated ceRNA networks in age-related changes of mouse thymus |
|
| Relations |
| BioSample |
SAMN13168748 |
| SRA |
SRX7079252 |
