|
| Status |
Public on May 08, 2019 |
| Title |
KO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
beta cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 x 129SV
age: 8 weeks
genotype: BetaRapKOGFP-/- without insulin pellet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Islets were isolated, digested into single cells and FACS. RNA was harvested using RNeasy micro kit and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
We used Hisat v2.0.4 to map the cleaned reads to the mouse mm10 reference genome.
After genome mapping, Stringtie v1.3.0 and TMM were used to caculate FPKM values.
Differentially expressed genes were identified using edgeR. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .
|
| |
|
| Submission date |
May 07, 2019 |
| Last update date |
May 09, 2019 |
| Contact name |
Qinglei Yin |
| E-mail(s) |
yinqinglei128@163.com
|
| Organization name |
Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine
|
| Street address |
Ruijin Second Road No.197
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE130792 |
Raptor determines β-cell identity and plasticity independent of metabolic state |
|
| Relations |
| BioSample |
SAMN11585342 |
| SRA |
SRX5799635 |
